Input: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/inputs/xbt Working: n-5-33.cluster.ucsf.bkslab.org:/scratch/xiaobo/418326/xbt-8058088.46 Result: /scratch/xiaobo/418326/xbt-8058088.46 Output: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbt 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/xbt mkdir: created directory `/scratch/xiaobo/418326' mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46' /scratch/xiaobo/418326/xbt-8058088.46 /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/418326/xbt-8058088.46/working' mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/protonate' Storing results in /scratch/xiaobo/418326/xbt-8058088.46/finished Working in /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 /scratch/xiaobo/418326/xbt-8058088.46/working/protonate /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Using inputs as protomers/tautomers. No processing done 453 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/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Bulk generating 3D conformations all protomers in /scratch/xiaobo/418326/xbt-8058088.46/working/3D mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/3D' We are using corina for 3D embeding debuging info:: /scratch/xiaobo/418326/xbt-8058088.46/working/protonate/xbt-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 ZINC001183097993 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building' mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for ZINC001183097993 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/1 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@]2(C1)COCCN(c1ncc(F)cn1)C2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097993.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001183097993 none O=C(N1CCC[C@]2(C1)COCCN(c1ncc(F)cn1)C2)[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.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 8, 1, 1, 15, 1, 8, 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, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 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, 7, 7] 0 hydrogens need 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, 11, 14, 14, 14, 14, 12, 14, 14, 14, 14, 14, 14, 17, 17, 14, 15, 17, 17, 14, 1, 1, 1, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 14, 13, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 17, 17, 14, 14, 8, 8, 15, 15, 15, 15, 15] 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]) total number of confs: 89 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 2) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/2 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/2' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@]2(C1)COCCN(c1ncc(F)cn1)C2)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097993.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001183097993 none O=C(N1CCC[C@]2(C1)COCCN(c1ncc(F)cn1)C2)[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.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 8, 1, 1, 15, 1, 8, 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, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 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, 7, 7] 0 hydrogens need 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, 13, 13, 13, 13, 11, 13, 13, 13, 13, 13, 13, 17, 17, 13, 14, 17, 17, 13, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 13, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 17, 17, 13, 13, 7, 7, 15, 15, 15, 15, 15] 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]) total number of confs: 91 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 3) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/3 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/3' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@]2(C1)COCCN(c1ncc(F)cn1)C2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097993.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001183097993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001183097993 none O=C(N1CCC[C@]2(C1)COCCN(c1ncc(F)cn1)C2)[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.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 8, 1, 1, 15, 1, 8, 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, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 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, 7, 7] 0 hydrogens need 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, 11, 14, 14, 14, 14, 12, 14, 14, 14, 14, 14, 14, 17, 17, 14, 15, 17, 17, 14, 1, 1, 1, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 14, 13, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 17, 17, 14, 14, 8, 8, 15, 15, 15, 15, 15] 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]) total number of confs: 89 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183097993 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/finished' Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993/2.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993 Building ZINC001183097993 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for ZINC001183097993 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 1) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/1: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@]2(C1)COCCN(c1ncc(F)cn1)C2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097993.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001183097993 none O=C(N1CCC[C@]2(C1)COCCN(c1ncc(F)cn1)C2)[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.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 8, 1, 1, 15, 1, 8, 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, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 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, 7, 7] 0 hydrogens need 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, 11, 14, 14, 14, 14, 12, 14, 14, 14, 14, 14, 14, 17, 17, 14, 15, 17, 17, 14, 1, 1, 1, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 14, 13, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 17, 17, 14, 14, 8, 8, 15, 15, 15, 15, 15] 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]) total number of confs: 89 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 2) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/2: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@]2(C1)COCCN(c1ncc(F)cn1)C2)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097993.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001183097993 none O=C(N1CCC[C@]2(C1)COCCN(c1ncc(F)cn1)C2)[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.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 8, 1, 1, 15, 1, 8, 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, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 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, 7, 7] 0 hydrogens need 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, 13, 13, 13, 13, 11, 13, 13, 13, 13, 13, 13, 17, 17, 13, 14, 17, 17, 13, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 13, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 17, 17, 13, 13, 7, 7, 15, 15, 15, 15, 15] 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]) total number of confs: 91 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 3) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/3: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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@]2(C1)COCCN(c1ncc(F)cn1)C2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097993.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001183097993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001183097993 none O=C(N1CCC[C@]2(C1)COCCN(c1ncc(F)cn1)C2)[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.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 8, 1, 1, 15, 1, 8, 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, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 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, 7, 7] 0 hydrogens need 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, 11, 14, 14, 14, 14, 12, 14, 14, 14, 14, 14, 14, 17, 17, 14, 15, 17, 17, 14, 1, 1, 1, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 14, 13, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 17, 17, 14, 14, 8, 8, 15, 15, 15, 15, 15] 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]) total number of confs: 89 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183097993 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993/2.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993 Building ZINC001183097993 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for ZINC001183097993 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 1) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/1: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@]2(C1)COCCN(c1ncc(F)cn1)C2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097993.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001183097993 none O=C(N1CCC[C@]2(C1)COCCN(c1ncc(F)cn1)C2)[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.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 8, 1, 1, 15, 1, 8, 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, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 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, 7, 7] 0 hydrogens need 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, 11, 14, 14, 14, 14, 12, 14, 14, 14, 14, 14, 14, 17, 17, 14, 15, 17, 17, 14, 1, 1, 1, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 14, 13, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 17, 17, 14, 14, 8, 8, 15, 15, 15, 15, 15] 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]) total number of confs: 89 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 2) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/2: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@]2(C1)COCCN(c1ncc(F)cn1)C2)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097993.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001183097993 none O=C(N1CCC[C@]2(C1)COCCN(c1ncc(F)cn1)C2)[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.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 8, 1, 1, 15, 1, 8, 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, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 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, 7, 7] 0 hydrogens need 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, 13, 13, 13, 13, 11, 13, 13, 13, 13, 13, 13, 17, 17, 13, 14, 17, 17, 13, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 13, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 17, 17, 13, 13, 7, 7, 15, 15, 15, 15, 15] 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]) total number of confs: 91 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 3) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/3: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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@]2(C1)COCCN(c1ncc(F)cn1)C2)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097993.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001183097993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001183097993 none O=C(N1CCC[C@]2(C1)COCCN(c1ncc(F)cn1)C2)[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.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 8, 1, 1, 15, 1, 8, 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, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 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, 7, 7] 0 hydrogens need 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, 11, 14, 14, 14, 14, 12, 14, 14, 14, 14, 14, 14, 17, 17, 14, 15, 17, 17, 14, 1, 1, 1, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 14, 13, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 17, 17, 14, 14, 8, 8, 15, 15, 15, 15, 15] 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]) total number of confs: 89 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183097993 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993/2.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183097993 Building ZINC001183098047 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098047' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098047 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183098047 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098047/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098047 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 4) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/4 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/4' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC[C@H]2CO[C@@]3(C2)COCCN(C(=O)[C@@]([O-])([SiH3])Cc2c[nH]c4ccccc24)C3)nn1) `ZINC001183098047.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183098047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098047/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001183098047 none Cc1ccc(NC[C@H]2CO[C@@]3(C2)COCCN(C(=O)[C@@]([O-])([SiH3])Cc2c[nH]c4ccccc24)C3)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 5, 7, 5, 12, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 35, 21, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11, 2, 11, 1, 1, 1, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12, 39, 39, 39, 39, 39, 39, 39, 35, 21, 21, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 5, 5, 8, 8, 8, 8, 8, 12, 12] 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, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 141 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098047 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098047/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098047 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 5) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/5 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/5' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC[C@H]2CO[C@@]3(C2)COCCN(C(=O)[C@]([O-])([SiH3])Cc2c[nH]c4ccccc24)C3)nn1) `ZINC001183098047.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183098047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098047/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001183098047 none Cc1ccc(NC[C@H]2CO[C@@]3(C2)COCCN(C(=O)[C@]([O-])([SiH3])Cc2c[nH]c4ccccc24)C3)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 5, 7, 5, 12, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 16, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 10, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 10, 30, 30, 30, 30, 30, 30, 30, 28, 16, 16, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 7, 7, 11, 11, 11, 11, 11, 10, 10] 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, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 117 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098047 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183098047 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098047/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098047/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098047 Building ZINC001183098047 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098047' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098047 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183098047 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098047/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098047 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 4) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1ccc(NC[C@H]2CO[C@@]3(C2)COCCN(C(=O)[C@@]([O-])([SiH3])Cc2c[nH]c4ccccc24)C3)nn1) `ZINC001183098047.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183098047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098047/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001183098047 none Cc1ccc(NC[C@H]2CO[C@@]3(C2)COCCN(C(=O)[C@@]([O-])([SiH3])Cc2c[nH]c4ccccc24)C3)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 5, 7, 5, 12, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 35, 21, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11, 2, 11, 1, 1, 1, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12, 39, 39, 39, 39, 39, 39, 39, 35, 21, 21, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 5, 5, 8, 8, 8, 8, 8, 12, 12] 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, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 141 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098047 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098047/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098047 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 5) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1ccc(NC[C@H]2CO[C@@]3(C2)COCCN(C(=O)[C@]([O-])([SiH3])Cc2c[nH]c4ccccc24)C3)nn1) `ZINC001183098047.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183098047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098047/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001183098047 none Cc1ccc(NC[C@H]2CO[C@@]3(C2)COCCN(C(=O)[C@]([O-])([SiH3])Cc2c[nH]c4ccccc24)C3)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 5, 7, 5, 12, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 16, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 10, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 10, 30, 30, 30, 30, 30, 30, 30, 28, 16, 16, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 7, 7, 11, 11, 11, 11, 11, 10, 10] 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, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 117 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098047 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183098047 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098047/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098047/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098047 Building ZINC001183098048 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098048' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098048 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183098048 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098048/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098048 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 6) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/6 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/6' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC[C@H]2CO[C@]3(C2)COCCN(C(=O)[C@@]([O-])([SiH3])Cc2c[nH]c4ccccc24)C3)nn1) `ZINC001183098048.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183098048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098048/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001183098048 none Cc1ccc(NC[C@H]2CO[C@]3(C2)COCCN(C(=O)[C@@]([O-])([SiH3])Cc2c[nH]c4ccccc24)C3)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 5, 7, 5, 12, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 7, 1, 1, 1, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 25, 25, 25, 25, 25, 25, 25, 24, 14, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 9, 13, 13, 13, 13, 13, 7, 7] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 115 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098048 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098048/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098048 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 7) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/7 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/7' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC[C@H]2CO[C@]3(C2)COCCN(C(=O)[C@]([O-])([SiH3])Cc2c[nH]c4ccccc24)C3)nn1) `ZINC001183098048.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183098048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098048/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001183098048 none Cc1ccc(NC[C@H]2CO[C@]3(C2)COCCN(C(=O)[C@]([O-])([SiH3])Cc2c[nH]c4ccccc24)C3)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 5, 7, 5, 12, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 16, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 8, 1, 1, 1, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 38, 38, 38, 38, 38, 38, 38, 31, 16, 16, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 6, 9, 9, 9, 9, 9, 8, 8] 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, 58, 59, 60, 61, 62]) total number of confs: 131 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098048 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183098048 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098048/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098048/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098048 Building ZINC001183098048 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098048' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098048 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183098048 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098048/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098048 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 6) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1ccc(NC[C@H]2CO[C@]3(C2)COCCN(C(=O)[C@@]([O-])([SiH3])Cc2c[nH]c4ccccc24)C3)nn1) `ZINC001183098048.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183098048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098048/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001183098048 none Cc1ccc(NC[C@H]2CO[C@]3(C2)COCCN(C(=O)[C@@]([O-])([SiH3])Cc2c[nH]c4ccccc24)C3)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 5, 7, 5, 12, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 7, 1, 1, 1, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 25, 25, 25, 25, 25, 25, 25, 24, 14, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 9, 13, 13, 13, 13, 13, 7, 7] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 115 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098048 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098048/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098048 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 7) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1ccc(NC[C@H]2CO[C@]3(C2)COCCN(C(=O)[C@]([O-])([SiH3])Cc2c[nH]c4ccccc24)C3)nn1) `ZINC001183098048.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183098048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098048/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001183098048 none Cc1ccc(NC[C@H]2CO[C@]3(C2)COCCN(C(=O)[C@]([O-])([SiH3])Cc2c[nH]c4ccccc24)C3)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 5, 7, 5, 12, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 16, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 8, 1, 1, 1, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 38, 38, 38, 38, 38, 38, 38, 31, 16, 16, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 6, 9, 9, 9, 9, 9, 8, 8] 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, 58, 59, 60, 61, 62]) total number of confs: 131 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098048 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183098048 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098048/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098048/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098048 Building ZINC001183098050 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098050' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098050 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183098050 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098050/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098050 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 8) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/8 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/8' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC[C@@H]2CO[C@]3(C2)COCCN(C(=O)[C@@]([O-])([SiH3])Cc2c[nH]c4ccccc24)C3)nn1) `ZINC001183098050.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183098050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098050/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001183098050 none Cc1ccc(NC[C@@H]2CO[C@]3(C2)COCCN(C(=O)[C@@]([O-])([SiH3])Cc2c[nH]c4ccccc24)C3)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 5, 7, 5, 12, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 35, 13, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 2, 5, 1, 1, 1, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 36, 36, 36, 36, 36, 36, 36, 35, 13, 13, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 9, 9, 9, 9, 9, 5, 5] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 136 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098050 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098050/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098050 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 9) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/9 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/9' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC[C@@H]2CO[C@]3(C2)COCCN(C(=O)[C@]([O-])([SiH3])Cc2c[nH]c4ccccc24)C3)nn1) `ZINC001183098050.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183098050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098050/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001183098050 none Cc1ccc(NC[C@@H]2CO[C@]3(C2)COCCN(C(=O)[C@]([O-])([SiH3])Cc2c[nH]c4ccccc24)C3)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 5, 7, 5, 12, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 32, 17, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 2, 7, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 36, 36, 36, 36, 36, 36, 36, 32, 17, 17, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 8, 8] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 130 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098050 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183098050 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098050/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098050/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098050 Building ZINC001183098050 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098050' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098050 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183098050 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098050/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098050 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 8) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1ccc(NC[C@@H]2CO[C@]3(C2)COCCN(C(=O)[C@@]([O-])([SiH3])Cc2c[nH]c4ccccc24)C3)nn1) `ZINC001183098050.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183098050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098050/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001183098050 none Cc1ccc(NC[C@@H]2CO[C@]3(C2)COCCN(C(=O)[C@@]([O-])([SiH3])Cc2c[nH]c4ccccc24)C3)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 5, 7, 5, 12, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 35, 13, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 2, 5, 1, 1, 1, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 36, 36, 36, 36, 36, 36, 36, 35, 13, 13, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 9, 9, 9, 9, 9, 5, 5] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 136 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098050 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098050/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098050 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 9) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1ccc(NC[C@@H]2CO[C@]3(C2)COCCN(C(=O)[C@]([O-])([SiH3])Cc2c[nH]c4ccccc24)C3)nn1) `ZINC001183098050.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183098050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098050/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001183098050 none Cc1ccc(NC[C@@H]2CO[C@]3(C2)COCCN(C(=O)[C@]([O-])([SiH3])Cc2c[nH]c4ccccc24)C3)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 5, 7, 5, 12, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 32, 17, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 2, 7, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 36, 36, 36, 36, 36, 36, 36, 32, 17, 17, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 8, 8] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 130 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098050 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183098050 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098050/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098050/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098050 Building ZINC001183098051 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098051' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098051 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183098051 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098051/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098051 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 10) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/10 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/10' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC[C@@H]2CO[C@@]3(C2)COCCN(C(=O)[C@@]([O-])([SiH3])Cc2c[nH]c4ccccc24)C3)nn1) `ZINC001183098051.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183098051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001183098051 none Cc1ccc(NC[C@@H]2CO[C@@]3(C2)COCCN(C(=O)[C@@]([O-])([SiH3])Cc2c[nH]c4ccccc24)C3)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 5, 7, 5, 12, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 16, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 2, 8, 1, 1, 1, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 9, 39, 39, 39, 39, 39, 39, 39, 28, 16, 16, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 7, 10, 10, 10, 10, 10, 9, 9] 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, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 128 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098051 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098051/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098051 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 11) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/11 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/11' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC[C@@H]2CO[C@@]3(C2)COCCN(C(=O)[C@]([O-])([SiH3])Cc2c[nH]c4ccccc24)C3)nn1) `ZINC001183098051.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183098051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098051/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001183098051 none Cc1ccc(NC[C@@H]2CO[C@@]3(C2)COCCN(C(=O)[C@]([O-])([SiH3])Cc2c[nH]c4ccccc24)C3)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 5, 7, 5, 12, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 13, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 7, 1, 1, 1, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 31, 31, 31, 31, 31, 31, 31, 27, 13, 13, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 8, 14, 14, 14, 14, 14, 7, 7] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 127 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098051 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183098051 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098051/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098051/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098051 Building ZINC001183098051 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098051' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098051 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183098051 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098051/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098051 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 10) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1ccc(NC[C@@H]2CO[C@@]3(C2)COCCN(C(=O)[C@@]([O-])([SiH3])Cc2c[nH]c4ccccc24)C3)nn1) `ZINC001183098051.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183098051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001183098051 none Cc1ccc(NC[C@@H]2CO[C@@]3(C2)COCCN(C(=O)[C@@]([O-])([SiH3])Cc2c[nH]c4ccccc24)C3)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 5, 7, 5, 12, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 16, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 2, 8, 1, 1, 1, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 9, 39, 39, 39, 39, 39, 39, 39, 28, 16, 16, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 7, 10, 10, 10, 10, 10, 9, 9] 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, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 128 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098051 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098051/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098051 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 11) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1ccc(NC[C@@H]2CO[C@@]3(C2)COCCN(C(=O)[C@]([O-])([SiH3])Cc2c[nH]c4ccccc24)C3)nn1) `ZINC001183098051.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183098051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098051/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001183098051 none Cc1ccc(NC[C@@H]2CO[C@@]3(C2)COCCN(C(=O)[C@]([O-])([SiH3])Cc2c[nH]c4ccccc24)C3)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 5, 7, 5, 12, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 13, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 7, 1, 1, 1, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 31, 31, 31, 31, 31, 31, 31, 27, 13, 13, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 8, 14, 14, 14, 14, 14, 7, 7] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 127 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098051 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183098051 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098051/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098051/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098051 Building ZINC001183098211 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098211' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098211 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183098211 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098211/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098211 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 12) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/12 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/12' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCOC[C@@]2(C[C@H](CNC(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)CO2)C1) `ZINC001183098211.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183098211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001183098211 none CC(C)(C)OC(=O)N1CCOC[C@@]2(C[C@H](CNC(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)CO2)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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 29, 33, 29, 29, 29, 29, 29, 29, 24, 10, 29, 3, 3, 1, 3, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29, 35, 35, 35, 35, 35, 35, 35, 35, 35, 29, 29, 29, 29, 29, 29, 29, 29, 10, 10, 3, 3, 3, 6, 6, 6, 6, 6, 29, 29, 29, 29] 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, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098211 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098211/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098211 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 13) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/13 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/13' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCOC[C@@]2(C[C@H](CNC(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)CO2)C1) `ZINC001183098211.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183098211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098211/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001183098211 none CC(C)(C)OC(=O)N1CCOC[C@@]2(C[C@H](CNC(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)CO2)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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 35, 32, 32, 32, 32, 32, 32, 30, 11, 31, 3, 3, 1, 3, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 31, 32, 32, 35, 35, 35, 35, 35, 35, 35, 35, 35, 32, 32, 32, 32, 32, 32, 32, 32, 11, 11, 3, 3, 3, 6, 6, 6, 6, 6, 32, 32, 32, 32] 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, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098211 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183098211 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098211/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098211/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098211 Building ZINC001183098211 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098211' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098211 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183098211 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098211/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098211 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 12) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/12: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCOC[C@@]2(C[C@H](CNC(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)CO2)C1) `ZINC001183098211.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183098211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001183098211 none CC(C)(C)OC(=O)N1CCOC[C@@]2(C[C@H](CNC(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)CO2)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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 29, 33, 29, 29, 29, 29, 29, 29, 24, 10, 29, 3, 3, 1, 3, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29, 35, 35, 35, 35, 35, 35, 35, 35, 35, 29, 29, 29, 29, 29, 29, 29, 29, 10, 10, 3, 3, 3, 6, 6, 6, 6, 6, 29, 29, 29, 29] 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, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098211 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098211/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098211 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 13) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/13: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCOC[C@@]2(C[C@H](CNC(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)CO2)C1) `ZINC001183098211.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183098211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098211/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001183098211 none CC(C)(C)OC(=O)N1CCOC[C@@]2(C[C@H](CNC(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)CO2)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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 35, 32, 32, 32, 32, 32, 32, 30, 11, 31, 3, 3, 1, 3, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 31, 32, 32, 35, 35, 35, 35, 35, 35, 35, 35, 35, 32, 32, 32, 32, 32, 32, 32, 32, 11, 11, 3, 3, 3, 6, 6, 6, 6, 6, 32, 32, 32, 32] 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, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098211 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183098211 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098211/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098211/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098211 Building ZINC001183098213 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098213' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098213 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183098213 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098213/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098213 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 14) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/14 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/14' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCOC[C@]2(C[C@@H](CNC(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)CO2)C1) `ZINC001183098213.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183098213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001183098213 none CC(C)(C)OC(=O)N1CCOC[C@]2(C[C@@H](CNC(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)CO2)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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 29, 34, 29, 29, 29, 29, 29, 29, 16, 8, 18, 2, 2, 1, 2, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 23, 29, 29, 34, 34, 34, 34, 34, 34, 34, 34, 34, 29, 29, 29, 29, 29, 29, 29, 29, 8, 8, 2, 2, 2, 3, 3, 3, 3, 3, 29, 29, 29, 29] 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, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098213 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098213/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098213 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 15) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/15 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/15' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCOC[C@]2(C[C@@H](CNC(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)CO2)C1) `ZINC001183098213.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183098213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098213/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001183098213 none CC(C)(C)OC(=O)N1CCOC[C@]2(C[C@@H](CNC(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)CO2)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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 27, 33, 27, 27, 27, 27, 27, 27, 15, 7, 19, 2, 2, 1, 2, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 26, 27, 27, 35, 35, 35, 35, 35, 35, 35, 35, 35, 27, 27, 27, 27, 27, 27, 27, 27, 7, 7, 2, 2, 2, 4, 4, 4, 4, 4, 27, 27, 27, 27] 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, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098213 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183098213 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098213/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098213/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098213 Building ZINC001183098213 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098213' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098213 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183098213 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098213/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098213 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 14) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC(C)(C)OC(=O)N1CCOC[C@]2(C[C@@H](CNC(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)CO2)C1) `ZINC001183098213.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183098213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001183098213 none CC(C)(C)OC(=O)N1CCOC[C@]2(C[C@@H](CNC(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)CO2)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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 29, 34, 29, 29, 29, 29, 29, 29, 16, 8, 18, 2, 2, 1, 2, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 23, 29, 29, 34, 34, 34, 34, 34, 34, 34, 34, 34, 29, 29, 29, 29, 29, 29, 29, 29, 8, 8, 2, 2, 2, 3, 3, 3, 3, 3, 29, 29, 29, 29] 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, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098213 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098213/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098213 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 15) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC(C)(C)OC(=O)N1CCOC[C@]2(C[C@@H](CNC(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)CO2)C1) `ZINC001183098213.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183098213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098213/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001183098213 none CC(C)(C)OC(=O)N1CCOC[C@]2(C[C@@H](CNC(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)CO2)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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 27, 33, 27, 27, 27, 27, 27, 27, 15, 7, 19, 2, 2, 1, 2, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 26, 27, 27, 35, 35, 35, 35, 35, 35, 35, 35, 35, 27, 27, 27, 27, 27, 27, 27, 27, 7, 7, 2, 2, 2, 4, 4, 4, 4, 4, 27, 27, 27, 27] 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, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098213 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183098213 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098213/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098213/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098213 Building ZINC001183098214 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098214' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098214 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183098214 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098214/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098214 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 16) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/16 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/16' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCOC[C@]2(C[C@H](CNC(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)CO2)C1) `ZINC001183098214.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183098214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001183098214 none CC(C)(C)OC(=O)N1CCOC[C@]2(C[C@H](CNC(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)CO2)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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 24, 30, 24, 24, 24, 24, 24, 24, 21, 13, 22, 2, 2, 1, 2, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 22, 24, 24, 31, 31, 31, 31, 31, 31, 31, 31, 31, 24, 24, 24, 24, 24, 24, 24, 24, 10, 10, 2, 2, 2, 4, 4, 4, 4, 4, 24, 24, 24, 24] 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, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 127 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098214 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098214/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098214 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 17) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/17 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/17' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCOC[C@]2(C[C@H](CNC(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)CO2)C1) `ZINC001183098214.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183098214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098214/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001183098214 none CC(C)(C)OC(=O)N1CCOC[C@]2(C[C@H](CNC(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)CO2)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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 20, 31, 20, 20, 20, 20, 20, 20, 12, 7, 18, 3, 3, 1, 3, 1, 1, 1, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 20, 20, 20, 34, 34, 34, 34, 34, 34, 34, 34, 34, 20, 20, 20, 20, 20, 20, 20, 20, 7, 7, 3, 4, 4, 7, 7, 7, 7, 7, 20, 20, 20, 20] 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, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098214 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183098214 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098214/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098214/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098214 Building ZINC001183098214 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098214' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098214 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183098214 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098214/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098214 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 16) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/16: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCOC[C@]2(C[C@H](CNC(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)CO2)C1) `ZINC001183098214.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183098214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001183098214 none CC(C)(C)OC(=O)N1CCOC[C@]2(C[C@H](CNC(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)CO2)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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 24, 30, 24, 24, 24, 24, 24, 24, 21, 13, 22, 2, 2, 1, 2, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 22, 24, 24, 31, 31, 31, 31, 31, 31, 31, 31, 31, 24, 24, 24, 24, 24, 24, 24, 24, 10, 10, 2, 2, 2, 4, 4, 4, 4, 4, 24, 24, 24, 24] 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, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 127 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098214 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098214/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098214 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 17) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/17: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCOC[C@]2(C[C@H](CNC(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)CO2)C1) `ZINC001183098214.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183098214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098214/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001183098214 none CC(C)(C)OC(=O)N1CCOC[C@]2(C[C@H](CNC(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)CO2)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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 20, 31, 20, 20, 20, 20, 20, 20, 12, 7, 18, 3, 3, 1, 3, 1, 1, 1, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 20, 20, 20, 34, 34, 34, 34, 34, 34, 34, 34, 34, 20, 20, 20, 20, 20, 20, 20, 20, 7, 7, 3, 4, 4, 7, 7, 7, 7, 7, 20, 20, 20, 20] 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, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098214 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183098214 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098214/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098214/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098214 Building ZINC001183098215 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098215' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098215 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183098215 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098215/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098215 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 18) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/18 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/18' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCOC[C@@]2(C[C@@H](CNC(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)CO2)C1) `ZINC001183098215.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183098215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001183098215 none CC(C)(C)OC(=O)N1CCOC[C@@]2(C[C@@H](CNC(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)CO2)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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 35, 31, 31, 31, 31, 31, 31, 28, 13, 31, 3, 3, 1, 3, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 27, 31, 31, 35, 35, 35, 35, 35, 35, 35, 35, 35, 31, 31, 31, 31, 31, 31, 31, 31, 9, 9, 3, 2, 2, 4, 4, 4, 4, 4, 31, 31, 31, 31] 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, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098215 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098215/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098215 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 19) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/19 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/19' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCOC[C@@]2(C[C@@H](CNC(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)CO2)C1) `ZINC001183098215.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183098215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098215/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001183098215 none CC(C)(C)OC(=O)N1CCOC[C@@]2(C[C@@H](CNC(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)CO2)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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 32, 25, 32, 25, 25, 25, 25, 25, 25, 25, 11, 25, 2, 2, 1, 2, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 22, 25, 25, 33, 33, 33, 33, 33, 33, 33, 33, 33, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 2, 2, 2, 4, 4, 4, 4, 4, 25, 25, 25, 25] 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, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098215 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183098215 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098215/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098215/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098215 Building ZINC001183098215 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098215' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098215 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183098215 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098215/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098215 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 18) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC(C)(C)OC(=O)N1CCOC[C@@]2(C[C@@H](CNC(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)CO2)C1) `ZINC001183098215.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183098215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001183098215 none CC(C)(C)OC(=O)N1CCOC[C@@]2(C[C@@H](CNC(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)CO2)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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 35, 31, 31, 31, 31, 31, 31, 28, 13, 31, 3, 3, 1, 3, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 27, 31, 31, 35, 35, 35, 35, 35, 35, 35, 35, 35, 31, 31, 31, 31, 31, 31, 31, 31, 9, 9, 3, 2, 2, 4, 4, 4, 4, 4, 31, 31, 31, 31] 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, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098215 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098215/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098215 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 19) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC(C)(C)OC(=O)N1CCOC[C@@]2(C[C@@H](CNC(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)CO2)C1) `ZINC001183098215.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183098215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098215/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001183098215 none CC(C)(C)OC(=O)N1CCOC[C@@]2(C[C@@H](CNC(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)CO2)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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 32, 25, 32, 25, 25, 25, 25, 25, 25, 25, 11, 25, 2, 2, 1, 2, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 22, 25, 25, 33, 33, 33, 33, 33, 33, 33, 33, 33, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 2, 2, 2, 4, 4, 4, 4, 4, 25, 25, 25, 25] 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, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098215 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183098215 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098215/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098215/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098215 Building ZINC001183098410 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098410' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098410 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183098410 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098410/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098410 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 20) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/20 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/20' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12)c1nc(N2CCOCC2)nc2c1CCNCC2) `ZINC001183098410.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183098410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098410/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001183098410 none CC(C)N(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12)c1nc(N2CCOCC2)nc2c1CCNCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 12, 5, 5, 8, 1, 1, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 19, 4, 1, 4, 1, 1, 1, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 13, 15, 16, 22, 37, 37, 37, 37, 37, 16, 16, 16, 16, 16, 16, 16, 16, 19, 19, 19, 19, 19, 19, 19, 4, 4, 7, 7, 7, 7, 7, 37, 37, 37, 37, 37, 37, 37, 37, 16, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 141 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098410 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098410/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098410 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 21) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/21 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/21' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12)c1nc(N2CCOCC2)nc2c1CCNCC2) `ZINC001183098410.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183098410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098410/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001183098410 none CC(C)N(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12)c1nc(N2CCOCC2)nc2c1CCNCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 12, 5, 5, 8, 1, 1, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 9, 22, 4, 1, 4, 1, 1, 1, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 13, 14, 15, 21, 37, 37, 37, 37, 37, 15, 15, 14, 15, 15, 15, 15, 15, 22, 22, 22, 22, 22, 22, 22, 6, 6, 11, 11, 11, 11, 11, 37, 37, 37, 37, 37, 37, 37, 37, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 157 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098410 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183098410 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098410/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098410/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098410 Building ZINC001183098410 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098410' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098410 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183098410 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098410/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098410 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 20) grep: /scratch/xiaobo/418326/xbt-8058088.46/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)N(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12)c1nc(N2CCOCC2)nc2c1CCNCC2) `ZINC001183098410.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183098410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098410/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001183098410 none CC(C)N(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12)c1nc(N2CCOCC2)nc2c1CCNCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 12, 5, 5, 8, 1, 1, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 19, 4, 1, 4, 1, 1, 1, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 13, 15, 16, 22, 37, 37, 37, 37, 37, 16, 16, 16, 16, 16, 16, 16, 16, 19, 19, 19, 19, 19, 19, 19, 4, 4, 7, 7, 7, 7, 7, 37, 37, 37, 37, 37, 37, 37, 37, 16, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 141 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098410 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098410/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098410 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 21) grep: /scratch/xiaobo/418326/xbt-8058088.46/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)N(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12)c1nc(N2CCOCC2)nc2c1CCNCC2) `ZINC001183098410.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183098410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098410/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001183098410 none CC(C)N(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12)c1nc(N2CCOCC2)nc2c1CCNCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 12, 5, 5, 8, 1, 1, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 9, 22, 4, 1, 4, 1, 1, 1, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 13, 14, 15, 21, 37, 37, 37, 37, 37, 15, 15, 14, 15, 15, 15, 15, 15, 22, 22, 22, 22, 22, 22, 22, 6, 6, 11, 11, 11, 11, 11, 37, 37, 37, 37, 37, 37, 37, 37, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 157 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098410 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183098410 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098410/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098410/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098410 Building ZINC001183098612 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098612' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098612 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183098612 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098612/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098612 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 22) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/22 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/22' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CN(c2ccc(N3CCOCC3)c(F)c2)C(=O)O1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183098612.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183098612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001183098612 none O=C(NC[C@H]1CN(c2ccc(N3CCOCC3)c(F)c2)C(=O)O1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'O.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, 5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 15, 1, 1, 11, 12, 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, 3, 7, 7, 7, 7, 7, 7, 6, 3, 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: [2, 1, 2, 2, 9, 10, 10, 10, 10, 15, 15, 15, 15, 35, 35, 35, 35, 35, 15, 15, 15, 10, 10, 10, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 6, 6, 10, 10, 15, 15, 35, 35, 35, 35, 35, 35, 35, 35, 15, 2, 2, 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, 57, 58, 59]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098612 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098612/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098612 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 23) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/23 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/23' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CN(c2ccc(N3CCOCC3)c(F)c2)C(=O)O1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183098612.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183098612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098612/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001183098612 none O=C(NC[C@H]1CN(c2ccc(N3CCOCC3)c(F)c2)C(=O)O1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'O.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, 5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 15, 1, 1, 11, 12, 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, 3, 7, 7, 7, 7, 7, 7, 6, 3, 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: [2, 1, 2, 2, 10, 13, 13, 13, 13, 20, 20, 20, 20, 36, 36, 36, 36, 36, 20, 20, 20, 13, 13, 13, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 6, 6, 13, 13, 20, 20, 36, 36, 36, 36, 36, 36, 36, 36, 20, 2, 2, 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, 57, 58, 59]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098612 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183098612 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098612/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098612/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098612 Building ZINC001183098612 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098612' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098612 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183098612 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098612/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098612 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 22) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: O=C(NC[C@H]1CN(c2ccc(N3CCOCC3)c(F)c2)C(=O)O1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183098612.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183098612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001183098612 none O=C(NC[C@H]1CN(c2ccc(N3CCOCC3)c(F)c2)C(=O)O1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'O.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, 5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 15, 1, 1, 11, 12, 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, 3, 7, 7, 7, 7, 7, 7, 6, 3, 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: [2, 1, 2, 2, 9, 10, 10, 10, 10, 15, 15, 15, 15, 35, 35, 35, 35, 35, 15, 15, 15, 10, 10, 10, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 6, 6, 10, 10, 15, 15, 35, 35, 35, 35, 35, 35, 35, 35, 15, 2, 2, 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, 57, 58, 59]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098612 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098612/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098612 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 23) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: O=C(NC[C@H]1CN(c2ccc(N3CCOCC3)c(F)c2)C(=O)O1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183098612.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183098612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098612/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001183098612 none O=C(NC[C@H]1CN(c2ccc(N3CCOCC3)c(F)c2)C(=O)O1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'O.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, 5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 15, 1, 1, 11, 12, 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, 3, 7, 7, 7, 7, 7, 7, 6, 3, 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: [2, 1, 2, 2, 10, 13, 13, 13, 13, 20, 20, 20, 20, 36, 36, 36, 36, 36, 20, 20, 20, 13, 13, 13, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 6, 6, 13, 13, 20, 20, 36, 36, 36, 36, 36, 36, 36, 36, 20, 2, 2, 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, 57, 58, 59]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098612 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183098612 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098612/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098612/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098612 Building ZINC001183098633 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098633' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098633 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183098633 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098633/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098633 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 24) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/24 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/24' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CN1CC[C@]2(CN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@H]2c2ccccc2)C1=O) `ZINC001183098633.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183098633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001183098633 none CN(C)C(=O)CN1CC[C@]2(CN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@H]2c2ccccc2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', '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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 31, 12, 12, 12, 12, 12, 12, 6, 1, 7, 1, 1, 1, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 31, 31, 31, 31, 31, 31, 29, 29, 12, 12, 12, 12, 12, 12, 8, 8, 13, 13, 13, 13, 13, 12, 12, 12, 12, 12, 12, 12] 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, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 141 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098633 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098633/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098633 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 25) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/25 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/25' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CN1CC[C@]2(CN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@H]2c2ccccc2)C1=O) `ZINC001183098633.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183098633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098633/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001183098633 none CN(C)C(=O)CN1CC[C@]2(CN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@H]2c2ccccc2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', '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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 28, 33, 13, 13, 13, 13, 13, 13, 6, 1, 7, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 33, 33, 33, 33, 33, 33, 28, 28, 13, 13, 13, 13, 13, 13, 7, 7, 11, 11, 11, 11, 11, 13, 13, 13, 13, 13, 13, 13] 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, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 138 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098633 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183098633 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098633/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098633/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098633 Building ZINC001183098633 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098633' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098633 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183098633 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098633/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098633 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 24) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CN(C)C(=O)CN1CC[C@]2(CN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@H]2c2ccccc2)C1=O) `ZINC001183098633.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183098633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001183098633 none CN(C)C(=O)CN1CC[C@]2(CN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@H]2c2ccccc2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', '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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 31, 12, 12, 12, 12, 12, 12, 6, 1, 7, 1, 1, 1, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 31, 31, 31, 31, 31, 31, 29, 29, 12, 12, 12, 12, 12, 12, 8, 8, 13, 13, 13, 13, 13, 12, 12, 12, 12, 12, 12, 12] 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, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 141 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098633 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098633/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098633 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 25) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CN(C)C(=O)CN1CC[C@]2(CN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@H]2c2ccccc2)C1=O) `ZINC001183098633.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183098633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098633/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001183098633 none CN(C)C(=O)CN1CC[C@]2(CN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@H]2c2ccccc2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', '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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 28, 33, 13, 13, 13, 13, 13, 13, 6, 1, 7, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 33, 33, 33, 33, 33, 33, 28, 28, 13, 13, 13, 13, 13, 13, 7, 7, 11, 11, 11, 11, 11, 13, 13, 13, 13, 13, 13, 13] 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, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 138 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098633 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183098633 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098633/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098633/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098633 Building ZINC001183098678 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098678' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098678 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183098678 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098678/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098678 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 26) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/26 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/26' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc2c(nc1c1cnn(C)c1)CCN(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c3ccccc13)CC2) `ZINC001183098678.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183098678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098678/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001183098678 none COC(=O)c1cc2c(nc1c1cnn(C)c1)CCN(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c3ccccc13)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 5, 1, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 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, 7] 0 hydrogens 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, 6, 17, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 19, 19, 6, 6, 3, 1, 6, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 17, 17, 17, 6, 19, 19, 19, 19, 19, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 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]) total number of confs: 86 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098678 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098678/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098678 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 27) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/27 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/27' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc2c(nc1c1cnn(C)c1)CCN(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c3ccccc13)CC2) `ZINC001183098678.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183098678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098678/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001183098678 none COC(=O)c1cc2c(nc1c1cnn(C)c1)CCN(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c3ccccc13)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 5, 1, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 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, 7] 0 hydrogens 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, 7, 19, 7, 7, 7, 7, 7, 7, 7, 25, 25, 25, 25, 25, 7, 7, 5, 1, 7, 1, 1, 1, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 19, 19, 19, 7, 25, 25, 25, 25, 25, 7, 7, 7, 7, 5, 5, 6, 6, 6, 6, 6, 7, 7, 7, 7] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 95 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098678 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183098678 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098678/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098678/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098678 Building ZINC001183098678 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098678' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098678 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183098678 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098678/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098678 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 26) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/26: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc2c(nc1c1cnn(C)c1)CCN(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c3ccccc13)CC2) `ZINC001183098678.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183098678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098678/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001183098678 none COC(=O)c1cc2c(nc1c1cnn(C)c1)CCN(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c3ccccc13)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 5, 1, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 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, 7] 0 hydrogens 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, 6, 17, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 19, 19, 6, 6, 3, 1, 6, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 17, 17, 17, 6, 19, 19, 19, 19, 19, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 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]) total number of confs: 86 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098678 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098678/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098678 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 27) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/27: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc2c(nc1c1cnn(C)c1)CCN(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c3ccccc13)CC2) `ZINC001183098678.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183098678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098678/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001183098678 none COC(=O)c1cc2c(nc1c1cnn(C)c1)CCN(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c3ccccc13)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 5, 1, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 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, 7] 0 hydrogens 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, 7, 19, 7, 7, 7, 7, 7, 7, 7, 25, 25, 25, 25, 25, 7, 7, 5, 1, 7, 1, 1, 1, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 19, 19, 19, 7, 25, 25, 25, 25, 25, 7, 7, 7, 7, 5, 5, 6, 6, 6, 6, 6, 7, 7, 7, 7] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 95 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098678 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183098678 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098678/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098678/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098678 Building ZINC001183098742 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098742' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098742 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183098742 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098742/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098742 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 28) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/28 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/28' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1ccncc1)[C@@H]1CCO[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@H]21) `ZINC001183098742.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183098742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001183098742 none O=C(NCCc1ccncc1)[C@@H]1CCO[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@H]21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 5, 7, 5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 16, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 1, 1, 1, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 7, 16, 16, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 8, 8, 8, 8, 8, 3, 3] 50 rigid atoms, others: [24, 25, 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, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 106 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098742 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098742/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098742 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 29) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/29 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/29' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1ccncc1)[C@@H]1CCO[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@H]21) `ZINC001183098742.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183098742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098742/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001183098742 none O=C(NCCc1ccncc1)[C@@H]1CCO[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@H]21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 5, 7, 5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 7, 7, 24, 30, 30, 30, 30, 30, 30, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 4, 4, 7, 24, 24, 30, 30, 30, 30, 30, 30, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 11, 11, 11, 11, 11, 4, 4] 50 rigid atoms, others: [24, 25, 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, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 154 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098742 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183098742 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098742/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098742/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098742 Building ZINC001183098742 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098742' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098742 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183098742 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098742/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098742 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 28) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: O=C(NCCc1ccncc1)[C@@H]1CCO[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@H]21) `ZINC001183098742.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183098742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001183098742 none O=C(NCCc1ccncc1)[C@@H]1CCO[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@H]21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 5, 7, 5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 16, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 1, 1, 1, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 7, 16, 16, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 8, 8, 8, 8, 8, 3, 3] 50 rigid atoms, others: [24, 25, 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, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 106 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098742 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098742/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098742 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 29) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: O=C(NCCc1ccncc1)[C@@H]1CCO[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@H]21) `ZINC001183098742.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183098742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098742/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001183098742 none O=C(NCCc1ccncc1)[C@@H]1CCO[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C[C@H]21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 5, 7, 5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 7, 7, 24, 30, 30, 30, 30, 30, 30, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 4, 4, 7, 24, 24, 30, 30, 30, 30, 30, 30, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 11, 11, 11, 11, 11, 4, 4] 50 rigid atoms, others: [24, 25, 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, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 154 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098742 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183098742 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098742/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098742/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098742 Building ZINC001183098999 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098999' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098999 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183098999 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098999/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098999 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 30) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/30 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/30' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ncnc(N(C(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)S(=O)(=O)c2ccc(N)cc2)c1OC) `ZINC001183098999.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183098999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098999/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001183098999 none COc1ncnc(N(C(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)S(=O)(=O)c2ccc(N)cc2)c1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'N.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', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 8, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 14, 11, 11, 1, 1, 1, 1, 8, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 16, 16, 16, 16, 16, 13, 6, 1, 6, 1, 1, 1, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 13, 19, 19, 19, 23, 23, 19, 19, 23, 23, 16, 16, 19, 19, 19, 19, 16, 7, 7, 10, 10, 10, 10, 10, 23, 23, 23, 23, 23, 23, 19, 19, 19] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098999 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098999/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098999 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 31) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/31 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/31' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ncnc(N(C(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)S(=O)(=O)c2ccc(N)cc2)c1OC) `ZINC001183098999.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183098999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098999/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001183098999 none COc1ncnc(N(C(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)S(=O)(=O)c2ccc(N)cc2)c1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'N.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', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 8, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 14, 11, 11, 1, 1, 1, 1, 8, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 15, 15, 15, 15, 15, 12, 6, 1, 6, 1, 1, 1, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 12, 19, 19, 19, 23, 23, 19, 19, 23, 23, 15, 15, 19, 18, 18, 18, 15, 7, 7, 9, 9, 9, 9, 9, 23, 23, 23, 23, 23, 23, 19, 19, 19] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098999 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183098999 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098999/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098999/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098999 Building ZINC001183098999 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098999' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098999 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183098999 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098999/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098999 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 30) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/30: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ncnc(N(C(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)S(=O)(=O)c2ccc(N)cc2)c1OC) `ZINC001183098999.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183098999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098999/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001183098999 none COc1ncnc(N(C(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)S(=O)(=O)c2ccc(N)cc2)c1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'N.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', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 8, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 14, 11, 11, 1, 1, 1, 1, 8, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 16, 16, 16, 16, 16, 13, 6, 1, 6, 1, 1, 1, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 13, 19, 19, 19, 23, 23, 19, 19, 23, 23, 16, 16, 19, 19, 19, 19, 16, 7, 7, 10, 10, 10, 10, 10, 23, 23, 23, 23, 23, 23, 19, 19, 19] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098999 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098999/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098999 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 31) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/31: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ncnc(N(C(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)S(=O)(=O)c2ccc(N)cc2)c1OC) `ZINC001183098999.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183098999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098999/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001183098999 none COc1ncnc(N(C(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)S(=O)(=O)c2ccc(N)cc2)c1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'N.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', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 8, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 14, 11, 11, 1, 1, 1, 1, 8, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 15, 15, 15, 15, 15, 12, 6, 1, 6, 1, 1, 1, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 12, 19, 19, 19, 23, 23, 19, 19, 23, 23, 15, 15, 19, 18, 18, 18, 15, 7, 7, 9, 9, 9, 9, 9, 23, 23, 23, 23, 23, 23, 19, 19, 19] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098999 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183098999 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098999/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098999/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183098999 Building ZINC001183099138 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099138' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099138 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183099138 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099138/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099138 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 32) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/32 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/32' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(N(C(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)S(=O)(=O)c2ccc(N)cc2)nn1) `ZINC001183099138.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099138/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001183099138 none COc1ccc(N(C(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)S(=O)(=O)c2ccc(N)cc2)nn1 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', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'N.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, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 14, 11, 11, 1, 1, 1, 1, 8, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 9, 4, 1, 4, 1, 1, 1, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 26, 26, 26, 30, 30, 26, 30, 30, 30, 19, 19, 19, 19, 19, 19, 19, 4, 4, 7, 7, 7, 7, 7, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099138 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099138/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099138 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 33) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/33 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/33' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(N(C(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)S(=O)(=O)c2ccc(N)cc2)nn1) `ZINC001183099138.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099138/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001183099138 none COc1ccc(N(C(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)S(=O)(=O)c2ccc(N)cc2)nn1 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', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'N.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, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 14, 11, 11, 1, 1, 1, 1, 8, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 3, 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: [14, 14, 14, 14, 14, 9, 3, 1, 3, 1, 1, 1, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 9, 22, 22, 22, 32, 32, 22, 24, 32, 32, 14, 14, 14, 14, 14, 14, 14, 7, 7, 10, 10, 10, 10, 10, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099138 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183099138 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099138/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099138/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099138 Building ZINC001183099138 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099138' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099138 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183099138 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099138/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099138 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 32) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc(N(C(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)S(=O)(=O)c2ccc(N)cc2)nn1) `ZINC001183099138.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099138/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001183099138 none COc1ccc(N(C(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)S(=O)(=O)c2ccc(N)cc2)nn1 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', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'N.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, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 14, 11, 11, 1, 1, 1, 1, 8, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 9, 4, 1, 4, 1, 1, 1, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 26, 26, 26, 30, 30, 26, 30, 30, 30, 19, 19, 19, 19, 19, 19, 19, 4, 4, 7, 7, 7, 7, 7, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099138 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099138/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099138 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 33) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc(N(C(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)S(=O)(=O)c2ccc(N)cc2)nn1) `ZINC001183099138.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099138/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001183099138 none COc1ccc(N(C(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)S(=O)(=O)c2ccc(N)cc2)nn1 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', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'N.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, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 14, 11, 11, 1, 1, 1, 1, 8, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 3, 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: [14, 14, 14, 14, 14, 9, 3, 1, 3, 1, 1, 1, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 9, 22, 22, 22, 32, 32, 22, 24, 32, 32, 14, 14, 14, 14, 14, 14, 14, 7, 7, 10, 10, 10, 10, 10, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099138 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183099138 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099138/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099138/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099138 Building ZINC001183099430 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099430' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099430 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183099430 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099430/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099430 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 34) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/34 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/34' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(N(C(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)S(=O)(=O)c2ccc(N)cc2)nc(OC)n1) `ZINC001183099430.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001183099430 none COc1cc(N(C(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)S(=O)(=O)c2ccc(N)cc2)nc(OC)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 14, 11, 11, 1, 1, 1, 1, 8, 1, 1, 8, 1, 12, 5, 8, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 14, 14, 14, 8, 2, 1, 2, 1, 1, 1, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 15, 15, 15, 22, 22, 20, 21, 22, 22, 14, 14, 14, 17, 14, 16, 16, 16, 14, 4, 4, 6, 6, 6, 6, 6, 22, 22, 22, 22, 22, 22, 17, 17, 17] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099430 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099430/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099430 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 35) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/35 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/35' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(N(C(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)S(=O)(=O)c2ccc(N)cc2)nc(OC)n1) `ZINC001183099430.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099430/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001183099430 none COc1cc(N(C(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)S(=O)(=O)c2ccc(N)cc2)nc(OC)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 14, 11, 11, 1, 1, 1, 1, 8, 1, 1, 8, 1, 12, 5, 8, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 14, 14, 14, 8, 2, 1, 2, 1, 1, 1, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 17, 17, 17, 24, 24, 17, 17, 24, 24, 14, 14, 14, 18, 14, 16, 16, 16, 14, 4, 4, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 18, 18, 18] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099430 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183099430 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099430/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099430/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099430 Building ZINC001183099430 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099430' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099430 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183099430 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099430/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099430 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 34) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(N(C(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)S(=O)(=O)c2ccc(N)cc2)nc(OC)n1) `ZINC001183099430.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001183099430 none COc1cc(N(C(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)S(=O)(=O)c2ccc(N)cc2)nc(OC)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 14, 11, 11, 1, 1, 1, 1, 8, 1, 1, 8, 1, 12, 5, 8, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 14, 14, 14, 8, 2, 1, 2, 1, 1, 1, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 15, 15, 15, 22, 22, 20, 21, 22, 22, 14, 14, 14, 17, 14, 16, 16, 16, 14, 4, 4, 6, 6, 6, 6, 6, 22, 22, 22, 22, 22, 22, 17, 17, 17] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099430 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099430/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099430 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 35) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(N(C(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)S(=O)(=O)c2ccc(N)cc2)nc(OC)n1) `ZINC001183099430.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099430/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001183099430 none COc1cc(N(C(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)S(=O)(=O)c2ccc(N)cc2)nc(OC)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 14, 11, 11, 1, 1, 1, 1, 8, 1, 1, 8, 1, 12, 5, 8, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 14, 14, 14, 8, 2, 1, 2, 1, 1, 1, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 17, 17, 17, 24, 24, 17, 17, 24, 24, 14, 14, 14, 18, 14, 16, 16, 16, 14, 4, 4, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 18, 18, 18] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099430 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183099430 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099430/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099430/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099430 Building ZINC001183099686 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099686' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099686 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183099686 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099686/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099686 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 36) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/36 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/36' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nc(Cl)c(I)c(NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)c1=O) `ZINC001183099686.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001183099686 none Cn1nc(Cl)c(I)c(NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)c1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'N.2', 'C.2', 'Cl', 'C.2', 'I', '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', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 16, 1, 18, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 4, 4, 1, 4, 1, 1, 1, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 17, 17, 17, 17, 17, 4, 8, 8, 18, 18, 18, 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]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099686 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099686/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099686 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 37) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/37 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/37' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nc(Cl)c(I)c(NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)c1=O) `ZINC001183099686.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099686/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001183099686 none Cn1nc(Cl)c(I)c(NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)c1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'N.2', 'C.2', 'Cl', 'C.2', 'I', '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', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 16, 1, 18, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 4, 4, 1, 4, 1, 1, 1, 8, 19, 19, 19, 19, 19, 19, 19, 19, 19, 17, 17, 17, 17, 17, 4, 8, 8, 19, 19, 19, 19, 19] 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: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099686 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183099686 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099686/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099686/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099686 Building ZINC001183099686 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099686' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099686 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183099686 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099686/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099686 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 36) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1nc(Cl)c(I)c(NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)c1=O) `ZINC001183099686.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001183099686 none Cn1nc(Cl)c(I)c(NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)c1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'N.2', 'C.2', 'Cl', 'C.2', 'I', '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', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 16, 1, 18, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 4, 4, 1, 4, 1, 1, 1, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 17, 17, 17, 17, 17, 4, 8, 8, 18, 18, 18, 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]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099686 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099686/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099686 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 37) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1nc(Cl)c(I)c(NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)c1=O) `ZINC001183099686.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099686/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001183099686 none Cn1nc(Cl)c(I)c(NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)c1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'N.2', 'C.2', 'Cl', 'C.2', 'I', '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', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 16, 1, 18, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 4, 4, 1, 4, 1, 1, 1, 8, 19, 19, 19, 19, 19, 19, 19, 19, 19, 17, 17, 17, 17, 17, 4, 8, 8, 19, 19, 19, 19, 19] 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: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099686 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183099686 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099686/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099686/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099686 Building ZINC001183099838 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099838' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099838 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183099838 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099838/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099838 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 38) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/38 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/38' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H](c1cnc(C(F)(F)F)nc1)N1CCOCC1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099838.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001183099838 none O=C(NC[C@H](c1cnc(C(F)(F)F)nc1)N1CCOCC1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 8, 1, 5, 15, 15, 15, 8, 1, 10, 5, 5, 12, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 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, 2, 10, 24, 24, 33, 33, 24, 33, 33, 33, 33, 33, 33, 24, 27, 27, 27, 27, 27, 1, 1, 1, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 10, 10, 33, 33, 27, 27, 27, 27, 27, 27, 27, 27, 4, 4, 7, 7, 7, 7, 7] 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]) total number of confs: 181 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099838 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099838/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099838 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 39) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/39 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/39' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H](c1cnc(C(F)(F)F)nc1)N1CCOCC1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099838.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099838/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001183099838 none O=C(NC[C@H](c1cnc(C(F)(F)F)nc1)N1CCOCC1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 8, 1, 5, 15, 15, 15, 8, 1, 10, 5, 5, 12, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 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, 2, 11, 21, 21, 32, 32, 21, 32, 32, 32, 32, 32, 32, 21, 22, 22, 22, 22, 22, 1, 1, 1, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 11, 11, 32, 32, 22, 22, 22, 22, 22, 22, 22, 22, 3, 3, 5, 5, 5, 5, 5] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 175 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099838 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183099838 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099838/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099838/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099838 Building ZINC001183099838 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099838' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099838 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183099838 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099838/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099838 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 38) grep: /scratch/xiaobo/418326/xbt-8058088.46/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(NC[C@H](c1cnc(C(F)(F)F)nc1)N1CCOCC1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099838.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001183099838 none O=C(NC[C@H](c1cnc(C(F)(F)F)nc1)N1CCOCC1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 8, 1, 5, 15, 15, 15, 8, 1, 10, 5, 5, 12, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 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, 2, 10, 24, 24, 33, 33, 24, 33, 33, 33, 33, 33, 33, 24, 27, 27, 27, 27, 27, 1, 1, 1, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 10, 10, 33, 33, 27, 27, 27, 27, 27, 27, 27, 27, 4, 4, 7, 7, 7, 7, 7] 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]) total number of confs: 181 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099838 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099838/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099838 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 39) grep: /scratch/xiaobo/418326/xbt-8058088.46/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(NC[C@H](c1cnc(C(F)(F)F)nc1)N1CCOCC1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099838.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099838/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001183099838 none O=C(NC[C@H](c1cnc(C(F)(F)F)nc1)N1CCOCC1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 8, 1, 5, 15, 15, 15, 8, 1, 10, 5, 5, 12, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 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, 2, 11, 21, 21, 32, 32, 21, 32, 32, 32, 32, 32, 32, 21, 22, 22, 22, 22, 22, 1, 1, 1, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 11, 11, 32, 32, 22, 22, 22, 22, 22, 22, 22, 22, 3, 3, 5, 5, 5, 5, 5] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 175 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099838 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183099838 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099838/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099838/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099838 Building ZINC001183099839 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099839' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099839 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183099839 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099839/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099839 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 40) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/40 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/40' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H](c1cnc(C(F)(F)F)nc1)N1CCOCC1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099839.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001183099839 none O=C(NC[C@@H](c1cnc(C(F)(F)F)nc1)N1CCOCC1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 8, 1, 5, 15, 15, 15, 8, 1, 10, 5, 5, 12, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 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, 2, 11, 21, 21, 32, 32, 21, 32, 32, 32, 32, 32, 32, 21, 22, 22, 22, 22, 22, 1, 1, 1, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 11, 11, 32, 32, 22, 22, 22, 22, 22, 22, 22, 22, 3, 3, 5, 5, 5, 5, 5] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 175 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099839 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099839/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099839 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 41) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/41 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/41' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H](c1cnc(C(F)(F)F)nc1)N1CCOCC1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099839.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099839/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001183099839 none O=C(NC[C@@H](c1cnc(C(F)(F)F)nc1)N1CCOCC1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 8, 1, 5, 15, 15, 15, 8, 1, 10, 5, 5, 12, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 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, 2, 9, 24, 24, 32, 32, 24, 32, 32, 32, 32, 32, 32, 24, 27, 27, 27, 27, 27, 1, 1, 1, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 9, 9, 32, 32, 27, 27, 27, 27, 27, 27, 27, 27, 4, 4, 7, 7, 7, 7, 7] 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]) total number of confs: 177 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099839 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183099839 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099839/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099839/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099839 Building ZINC001183099839 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099839' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099839 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183099839 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099839/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099839 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 40) grep: /scratch/xiaobo/418326/xbt-8058088.46/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(NC[C@@H](c1cnc(C(F)(F)F)nc1)N1CCOCC1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099839.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001183099839 none O=C(NC[C@@H](c1cnc(C(F)(F)F)nc1)N1CCOCC1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 8, 1, 5, 15, 15, 15, 8, 1, 10, 5, 5, 12, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 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, 2, 11, 21, 21, 32, 32, 21, 32, 32, 32, 32, 32, 32, 21, 22, 22, 22, 22, 22, 1, 1, 1, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 11, 11, 32, 32, 22, 22, 22, 22, 22, 22, 22, 22, 3, 3, 5, 5, 5, 5, 5] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 175 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099839 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099839/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099839 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 41) grep: /scratch/xiaobo/418326/xbt-8058088.46/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(NC[C@@H](c1cnc(C(F)(F)F)nc1)N1CCOCC1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099839.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099839/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001183099839 none O=C(NC[C@@H](c1cnc(C(F)(F)F)nc1)N1CCOCC1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 8, 1, 5, 15, 15, 15, 8, 1, 10, 5, 5, 12, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 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, 2, 9, 24, 24, 32, 32, 24, 32, 32, 32, 32, 32, 32, 24, 27, 27, 27, 27, 27, 1, 1, 1, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 9, 9, 32, 32, 27, 27, 27, 27, 27, 27, 27, 27, 4, 4, 7, 7, 7, 7, 7] 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]) total number of confs: 177 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099839 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183099839 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099839/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099839/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183099839 Building ZINC001183100373 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183100373' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183100373 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183100373 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183100373/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183100373 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 42) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/42 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/42' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CCCCN)N(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12)S(=O)(=O)c1ccc(C)cc1) `ZINC001183100373.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183100373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183100373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001183100373 none COC(=O)[C@H](CCCCN)N(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12)S(=O)(=O)c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.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', 'S.o2', 'O.2', 'O.2', '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, 12, 1, 11, 5, 7, 5, 5, 5, 5, 10, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 14, 11, 11, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 2, 2, 6, 8, 2, 1, 2, 1, 1, 1, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 4, 4, 4, 7, 7, 6, 6, 7, 7, 4, 4, 4, 2, 2, 2, 2, 6, 6, 8, 8, 8, 8, 6, 6, 9, 9, 9, 9, 9, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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: 89 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183100373 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183100373/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183100373 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 43) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/43 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/43' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CCCCN)N(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12)S(=O)(=O)c1ccc(C)cc1) `ZINC001183100373.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183100373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183100373/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001183100373 none COC(=O)[C@H](CCCCN)N(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12)S(=O)(=O)c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.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', 'S.o2', 'O.2', 'O.2', '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, 12, 1, 11, 5, 7, 5, 5, 5, 5, 10, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 14, 11, 11, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 3, 5, 2, 3, 3, 5, 5, 11, 11, 2, 1, 2, 1, 1, 1, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 6, 6, 6, 10, 10, 9, 9, 10, 10, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 11, 11, 11, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183100373 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183100373 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183100373/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183100373/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183100373 Building ZINC001183100373 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183100373' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183100373 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183100373 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183100373/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183100373 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 42) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COC(=O)[C@H](CCCCN)N(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12)S(=O)(=O)c1ccc(C)cc1) `ZINC001183100373.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183100373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183100373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001183100373 none COC(=O)[C@H](CCCCN)N(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12)S(=O)(=O)c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.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', 'S.o2', 'O.2', 'O.2', '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, 12, 1, 11, 5, 7, 5, 5, 5, 5, 10, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 14, 11, 11, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 2, 2, 6, 8, 2, 1, 2, 1, 1, 1, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 4, 4, 4, 7, 7, 6, 6, 7, 7, 4, 4, 4, 2, 2, 2, 2, 6, 6, 8, 8, 8, 8, 6, 6, 9, 9, 9, 9, 9, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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: 89 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183100373 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183100373/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183100373 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 43) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COC(=O)[C@H](CCCCN)N(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12)S(=O)(=O)c1ccc(C)cc1) `ZINC001183100373.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183100373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183100373/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001183100373 none COC(=O)[C@H](CCCCN)N(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12)S(=O)(=O)c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.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', 'S.o2', 'O.2', 'O.2', '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, 12, 1, 11, 5, 7, 5, 5, 5, 5, 10, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 14, 11, 11, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 3, 5, 2, 3, 3, 5, 5, 11, 11, 2, 1, 2, 1, 1, 1, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 6, 6, 6, 10, 10, 9, 9, 10, 10, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 11, 11, 11, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183100373 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183100373 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183100373/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183100373/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183100373 Building ZINC001183100862 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183100862' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183100862 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183100862 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183100862/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183100862 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 44) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/44 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/44' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)CCOCCOCCOCCNC(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183100862.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183100862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183100862/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001183100862 none CC(C)(C)OC(=O)CCOCCOCCOCCNC(=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', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 12, 5, 5, 12, 5, 5, 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, 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, 5, 7, 7, 3, 7, 7, 3, 7, 7, 3, 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: [40, 40, 40, 40, 40, 28, 40, 21, 16, 15, 15, 13, 12, 12, 8, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 40, 40, 40, 40, 40, 40, 40, 40, 40, 28, 28, 21, 21, 15, 15, 15, 15, 12, 12, 12, 12, 3, 3, 3, 3, 1, 2, 2, 3, 3, 3, 3, 3] 50 rigid atoms, others: [17, 18, 19, 20, 21, 22, 23, 59] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183100862 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183100862/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183100862 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 45) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/45 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/45' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)CCOCCOCCOCCNC(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183100862.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183100862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183100862/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001183100862 none CC(C)(C)OC(=O)CCOCCOCCOCCNC(=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', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 12, 5, 5, 12, 5, 5, 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, 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, 5, 7, 7, 3, 7, 7, 3, 7, 7, 3, 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: [42, 42, 42, 42, 42, 30, 42, 23, 17, 16, 16, 14, 13, 13, 9, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 42, 42, 42, 42, 42, 42, 42, 42, 42, 30, 30, 23, 23, 16, 16, 16, 16, 13, 13, 13, 13, 3, 3, 3, 3, 1, 2, 2, 3, 3, 3, 3, 3] 50 rigid atoms, others: [17, 18, 19, 20, 21, 22, 23, 59] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183100862 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183100862 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183100862/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183100862/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183100862 Building ZINC001183100862 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183100862' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183100862 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183100862 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183100862/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183100862 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 44) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC(C)(C)OC(=O)CCOCCOCCOCCNC(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183100862.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183100862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183100862/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001183100862 none CC(C)(C)OC(=O)CCOCCOCCOCCNC(=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', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 12, 5, 5, 12, 5, 5, 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, 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, 5, 7, 7, 3, 7, 7, 3, 7, 7, 3, 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: [40, 40, 40, 40, 40, 28, 40, 21, 16, 15, 15, 13, 12, 12, 8, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 40, 40, 40, 40, 40, 40, 40, 40, 40, 28, 28, 21, 21, 15, 15, 15, 15, 12, 12, 12, 12, 3, 3, 3, 3, 1, 2, 2, 3, 3, 3, 3, 3] 50 rigid atoms, others: [17, 18, 19, 20, 21, 22, 23, 59] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183100862 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183100862/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183100862 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 45) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC(C)(C)OC(=O)CCOCCOCCOCCNC(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183100862.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183100862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183100862/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001183100862 none CC(C)(C)OC(=O)CCOCCOCCOCCNC(=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', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 5, 12, 5, 5, 12, 5, 5, 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, 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, 5, 7, 7, 3, 7, 7, 3, 7, 7, 3, 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: [42, 42, 42, 42, 42, 30, 42, 23, 17, 16, 16, 14, 13, 13, 9, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 42, 42, 42, 42, 42, 42, 42, 42, 42, 30, 30, 23, 23, 16, 16, 16, 16, 13, 13, 13, 13, 3, 3, 3, 3, 1, 2, 2, 3, 3, 3, 3, 3] 50 rigid atoms, others: [17, 18, 19, 20, 21, 22, 23, 59] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183100862 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183100862 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183100862/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183100862/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183100862 Building ZINC001183356812 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183356812' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183356812 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183356812 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183356812/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183356812 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 46) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/46 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/46' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(S(=O)(=O)c3cccc4cnccc43)CC2)cc1) `ZINC001183356812.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183356812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183356812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183356812 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(S(=O)(=O)c3cccc4cnccc43)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 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] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 2, 3, 4, 6, 6, 6, 6, 6, 9, 9, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 6, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 6, 20, 20, 20, 20, 20, 20, 6, 6, 6, 6, 2, 2] 20 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]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183356812 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183356812/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183356812 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 47) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/47 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/47' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(S(=O)(=O)c3cccc4cnccc43)CC2)cc1) `ZINC001183356812.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183356812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183356812/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183356812 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(S(=O)(=O)c3cccc4cnccc43)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 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] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 2, 3, 3, 5, 5, 5, 5, 5, 9, 9, 9, 26, 26, 26, 26, 26, 26, 26, 26, 26, 5, 5, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 26, 26, 26, 26, 26, 26, 5, 5, 5, 5, 2, 2] 26 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]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183356812 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183356812 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183356812/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183356812/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183356812 Building ZINC001183356812 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183356812' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183356812 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183356812 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183356812/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183356812 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 46) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/46: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(S(=O)(=O)c3cccc4cnccc43)CC2)cc1) `ZINC001183356812.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183356812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183356812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183356812 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCN(S(=O)(=O)c3cccc4cnccc43)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 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] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 2, 3, 4, 6, 6, 6, 6, 6, 9, 9, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 6, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 6, 20, 20, 20, 20, 20, 20, 6, 6, 6, 6, 2, 2] 20 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]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183356812 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183356812/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183356812 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 47) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/47: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(S(=O)(=O)c3cccc4cnccc43)CC2)cc1) `ZINC001183356812.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183356812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183356812/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183356812 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCN(S(=O)(=O)c3cccc4cnccc43)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 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] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 2, 3, 3, 5, 5, 5, 5, 5, 9, 9, 9, 26, 26, 26, 26, 26, 26, 26, 26, 26, 5, 5, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 26, 26, 26, 26, 26, 26, 5, 5, 5, 5, 2, 2] 26 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]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183356812 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183356812 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183356812/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183356812/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183356812 Building ZINC001183357403 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001183357403 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 48) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/48 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/48' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@H]3[C@H](C[C@@H](Cn4cncn4)N3c3nccs3)C2)cc1) `ZINC001183357403.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183357403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183357403 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@H]3[C@H](C[C@@H](Cn4cncn4)N3c3nccs3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.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, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 7, 5, 8, 1, 8, 1, 8, 8, 1, 8, 1, 1, 14, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 3, 1, 1, 1, 2, 7, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 27, 40, 40, 40, 40, 13, 13, 26, 26, 26, 26, 13, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 27, 27, 40, 40, 26, 26, 13, 13, 3, 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, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 49) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/49 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/49' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@H]3[C@H](C[C@@H](Cn4cncn4)N3c3nccs3)C2)cc1) `ZINC001183357403.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183357403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183357403 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@H]3[C@H](C[C@@H](Cn4cncn4)N3c3nccs3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.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, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 7, 5, 8, 1, 8, 1, 8, 8, 1, 8, 1, 1, 14, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 4, 4, 1, 1, 1, 2, 5, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 23, 35, 35, 35, 35, 10, 10, 23, 23, 23, 23, 10, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 23, 23, 35, 35, 23, 23, 10, 10, 4, 4] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 50) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/50 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/50' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@H]3[C@H](C[C@@H](Cn4cncn4)N3c3nccs3)C2)cc1) `ZINC001183357403.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001183357403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183357403 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@H]3[C@H](C[C@@H](Cn4cncn4)N3c3nccs3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.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, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 7, 5, 8, 1, 8, 1, 8, 8, 1, 8, 1, 1, 14, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 3, 1, 1, 1, 2, 7, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 27, 40, 40, 40, 40, 13, 13, 26, 26, 26, 26, 13, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 27, 27, 40, 40, 26, 26, 13, 13, 3, 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, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 51) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/51 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/51' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@H]3[C@H](C[C@@H](Cn4cncn4)N3c3nccs3)C2)cc1) `ZINC001183357403.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001183357403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183357403 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@H]3[C@H](C[C@@H](Cn4cncn4)N3c3nccs3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.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, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 7, 5, 8, 1, 8, 1, 8, 8, 1, 8, 1, 1, 14, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 4, 4, 1, 1, 1, 2, 5, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 23, 35, 35, 35, 35, 10, 10, 23, 23, 23, 23, 10, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 23, 23, 35, 35, 23, 23, 10, 10, 4, 4] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183357403 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403 Building ZINC001183357403 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001183357403 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 48) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@H]3[C@H](C[C@@H](Cn4cncn4)N3c3nccs3)C2)cc1) `ZINC001183357403.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183357403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183357403 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@H]3[C@H](C[C@@H](Cn4cncn4)N3c3nccs3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.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, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 7, 5, 8, 1, 8, 1, 8, 8, 1, 8, 1, 1, 14, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 3, 1, 1, 1, 2, 7, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 27, 40, 40, 40, 40, 13, 13, 26, 26, 26, 26, 13, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 27, 27, 40, 40, 26, 26, 13, 13, 3, 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, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 49) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@H]3[C@H](C[C@@H](Cn4cncn4)N3c3nccs3)C2)cc1) `ZINC001183357403.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183357403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183357403 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@H]3[C@H](C[C@@H](Cn4cncn4)N3c3nccs3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.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, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 7, 5, 8, 1, 8, 1, 8, 8, 1, 8, 1, 1, 14, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 4, 4, 1, 1, 1, 2, 5, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 23, 35, 35, 35, 35, 10, 10, 23, 23, 23, 23, 10, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 23, 23, 35, 35, 23, 23, 10, 10, 4, 4] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 50) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/50: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CC[C@H]3[C@H](C[C@@H](Cn4cncn4)N3c3nccs3)C2)cc1) `ZINC001183357403.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001183357403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183357403 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@H]3[C@H](C[C@@H](Cn4cncn4)N3c3nccs3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.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, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 7, 5, 8, 1, 8, 1, 8, 8, 1, 8, 1, 1, 14, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 3, 1, 1, 1, 2, 7, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 27, 40, 40, 40, 40, 13, 13, 26, 26, 26, 26, 13, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 27, 27, 40, 40, 26, 26, 13, 13, 3, 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, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 51) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/51: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CC[C@H]3[C@H](C[C@@H](Cn4cncn4)N3c3nccs3)C2)cc1) `ZINC001183357403.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001183357403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183357403 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@H]3[C@H](C[C@@H](Cn4cncn4)N3c3nccs3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.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, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 7, 5, 8, 1, 8, 1, 8, 8, 1, 8, 1, 1, 14, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 4, 4, 1, 1, 1, 2, 5, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 23, 35, 35, 35, 35, 10, 10, 23, 23, 23, 23, 10, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 23, 23, 35, 35, 23, 23, 10, 10, 4, 4] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183357403 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403 Building ZINC001183357403 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001183357403 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 48) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@H]3[C@H](C[C@@H](Cn4cncn4)N3c3nccs3)C2)cc1) `ZINC001183357403.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183357403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183357403 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@H]3[C@H](C[C@@H](Cn4cncn4)N3c3nccs3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.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, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 7, 5, 8, 1, 8, 1, 8, 8, 1, 8, 1, 1, 14, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 3, 1, 1, 1, 2, 7, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 27, 40, 40, 40, 40, 13, 13, 26, 26, 26, 26, 13, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 27, 27, 40, 40, 26, 26, 13, 13, 3, 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, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 49) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@H]3[C@H](C[C@@H](Cn4cncn4)N3c3nccs3)C2)cc1) `ZINC001183357403.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183357403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183357403 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@H]3[C@H](C[C@@H](Cn4cncn4)N3c3nccs3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.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, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 7, 5, 8, 1, 8, 1, 8, 8, 1, 8, 1, 1, 14, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 4, 4, 1, 1, 1, 2, 5, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 23, 35, 35, 35, 35, 10, 10, 23, 23, 23, 23, 10, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 23, 23, 35, 35, 23, 23, 10, 10, 4, 4] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 50) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/50: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CC[C@H]3[C@H](C[C@@H](Cn4cncn4)N3c3nccs3)C2)cc1) `ZINC001183357403.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001183357403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183357403 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@H]3[C@H](C[C@@H](Cn4cncn4)N3c3nccs3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.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, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 7, 5, 8, 1, 8, 1, 8, 8, 1, 8, 1, 1, 14, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 3, 1, 1, 1, 2, 7, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 27, 40, 40, 40, 40, 13, 13, 26, 26, 26, 26, 13, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 27, 27, 40, 40, 26, 26, 13, 13, 3, 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, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 51) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/51: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CC[C@H]3[C@H](C[C@@H](Cn4cncn4)N3c3nccs3)C2)cc1) `ZINC001183357403.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001183357403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183357403 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@H]3[C@H](C[C@@H](Cn4cncn4)N3c3nccs3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.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, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 7, 5, 8, 1, 8, 1, 8, 8, 1, 8, 1, 1, 14, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 4, 4, 1, 1, 1, 2, 5, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 23, 35, 35, 35, 35, 10, 10, 23, 23, 23, 23, 10, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 23, 23, 35, 35, 23, 23, 10, 10, 4, 4] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183357403 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403 Building ZINC001183357403 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001183357403 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 48) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@H]3[C@H](C[C@@H](Cn4cncn4)N3c3nccs3)C2)cc1) `ZINC001183357403.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183357403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183357403 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@H]3[C@H](C[C@@H](Cn4cncn4)N3c3nccs3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.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, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 7, 5, 8, 1, 8, 1, 8, 8, 1, 8, 1, 1, 14, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 3, 1, 1, 1, 2, 7, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 27, 40, 40, 40, 40, 13, 13, 26, 26, 26, 26, 13, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 27, 27, 40, 40, 26, 26, 13, 13, 3, 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, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 49) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@H]3[C@H](C[C@@H](Cn4cncn4)N3c3nccs3)C2)cc1) `ZINC001183357403.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183357403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183357403 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@H]3[C@H](C[C@@H](Cn4cncn4)N3c3nccs3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.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, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 7, 5, 8, 1, 8, 1, 8, 8, 1, 8, 1, 1, 14, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 4, 4, 1, 1, 1, 2, 5, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 23, 35, 35, 35, 35, 10, 10, 23, 23, 23, 23, 10, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 23, 23, 35, 35, 23, 23, 10, 10, 4, 4] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 50) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/50: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CC[C@H]3[C@H](C[C@@H](Cn4cncn4)N3c3nccs3)C2)cc1) `ZINC001183357403.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001183357403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183357403 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@H]3[C@H](C[C@@H](Cn4cncn4)N3c3nccs3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.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, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 7, 5, 8, 1, 8, 1, 8, 8, 1, 8, 1, 1, 14, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 3, 1, 1, 1, 2, 7, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 27, 40, 40, 40, 40, 13, 13, 26, 26, 26, 26, 13, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 27, 27, 40, 40, 26, 26, 13, 13, 3, 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, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 51) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/51: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CC[C@H]3[C@H](C[C@@H](Cn4cncn4)N3c3nccs3)C2)cc1) `ZINC001183357403.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001183357403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183357403 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@H]3[C@H](C[C@@H](Cn4cncn4)N3c3nccs3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.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, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 7, 5, 8, 1, 8, 1, 8, 8, 1, 8, 1, 1, 14, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 4, 4, 1, 1, 1, 2, 5, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 23, 35, 35, 35, 35, 10, 10, 23, 23, 23, 23, 10, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 23, 23, 35, 35, 23, 23, 10, 10, 4, 4] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183357403 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183357403 Building ZINC001183358106 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358106' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358106 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183358106 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358106/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358106 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 52) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/52 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/52' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC3(CC2)OCC(=O)N(Cc2cccc(C)n2)[C@@H]3C)cc1) `ZINC001183358106.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183358106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183358106 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC3(CC2)OCC(=O)N(Cc2cccc(C)n2)[C@@H]3C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 8, 5, 7, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 2, 2, 1, 1, 1, 1, 3, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 28, 50, 50, 50, 50, 50, 50, 10, 10, 10, 2, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 28, 28, 50, 50, 50, 50, 50, 50, 10, 10, 10, 2, 2] 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: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358106 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358106/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358106 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 53) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/53 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/53' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC3(CC2)OCC(=O)N(Cc2cccc(C)n2)[C@@H]3C)cc1) `ZINC001183358106.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183358106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358106/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183358106 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC3(CC2)OCC(=O)N(Cc2cccc(C)n2)[C@@H]3C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 8, 5, 7, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 5, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 27, 50, 50, 50, 50, 50, 50, 12, 12, 12, 2, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 27, 27, 50, 50, 50, 50, 50, 50, 12, 12, 12, 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: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358106 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183358106 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358106/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358106/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358106 Building ZINC001183358106 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358106' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358106 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183358106 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358106/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358106 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 52) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC3(CC2)OCC(=O)N(Cc2cccc(C)n2)[C@@H]3C)cc1) `ZINC001183358106.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183358106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183358106 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC3(CC2)OCC(=O)N(Cc2cccc(C)n2)[C@@H]3C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 8, 5, 7, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 2, 2, 1, 1, 1, 1, 3, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 28, 50, 50, 50, 50, 50, 50, 10, 10, 10, 2, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 28, 28, 50, 50, 50, 50, 50, 50, 10, 10, 10, 2, 2] 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: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358106 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358106/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358106 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 53) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC3(CC2)OCC(=O)N(Cc2cccc(C)n2)[C@@H]3C)cc1) `ZINC001183358106.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183358106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358106/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183358106 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC3(CC2)OCC(=O)N(Cc2cccc(C)n2)[C@@H]3C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 8, 5, 7, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 5, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 27, 50, 50, 50, 50, 50, 50, 12, 12, 12, 2, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 27, 27, 50, 50, 50, 50, 50, 50, 12, 12, 12, 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: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358106 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183358106 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358106/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358106/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358106 Building ZINC001183358107 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358107' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358107 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183358107 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358107/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358107 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 54) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/54 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/54' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC3(CC2)OCC(=O)N(Cc2cccc(C)n2)[C@H]3C)cc1) `ZINC001183358107.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183358107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183358107 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC3(CC2)OCC(=O)N(Cc2cccc(C)n2)[C@H]3C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 8, 5, 7, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 2, 2, 1, 1, 1, 1, 4, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 25, 50, 50, 50, 50, 50, 50, 10, 10, 10, 2, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 25, 25, 50, 50, 50, 50, 50, 50, 10, 10, 10, 2, 2] 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: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358107 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358107/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358107 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 55) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/55 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/55' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC3(CC2)OCC(=O)N(Cc2cccc(C)n2)[C@H]3C)cc1) `ZINC001183358107.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183358107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358107/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183358107 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC3(CC2)OCC(=O)N(Cc2cccc(C)n2)[C@H]3C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 8, 5, 7, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 4, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 28, 50, 50, 50, 50, 50, 50, 12, 12, 12, 2, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 28, 28, 50, 50, 50, 50, 50, 50, 12, 12, 12, 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: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358107 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183358107 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358107/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358107/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358107 Building ZINC001183358107 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358107' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358107 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183358107 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358107/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358107 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 54) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC3(CC2)OCC(=O)N(Cc2cccc(C)n2)[C@H]3C)cc1) `ZINC001183358107.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183358107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183358107 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC3(CC2)OCC(=O)N(Cc2cccc(C)n2)[C@H]3C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 8, 5, 7, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 2, 2, 1, 1, 1, 1, 4, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 25, 50, 50, 50, 50, 50, 50, 10, 10, 10, 2, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 25, 25, 50, 50, 50, 50, 50, 50, 10, 10, 10, 2, 2] 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: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358107 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358107/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358107 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 55) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC3(CC2)OCC(=O)N(Cc2cccc(C)n2)[C@H]3C)cc1) `ZINC001183358107.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183358107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358107/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183358107 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC3(CC2)OCC(=O)N(Cc2cccc(C)n2)[C@H]3C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 8, 5, 7, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 4, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 28, 50, 50, 50, 50, 50, 50, 12, 12, 12, 2, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 28, 28, 50, 50, 50, 50, 50, 50, 12, 12, 12, 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: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358107 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183358107 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358107/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358107/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358107 Building ZINC001183358282 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358282' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358282 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183358282 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358282/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358282 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 56) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/56 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/56' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2Cc3ncnn3C3(CCN(C(=O)OC(C)(C)C)CC3)C2)cc1) `ZINC001183358282.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183358282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183358282 none COc1ccc([C@]([O-])([SiH3])C(=O)N2Cc3ncnn3C3(CCN(C(=O)OC(C)(C)C)CC3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 8, 5, 5, 5, 8, 1, 11, 12, 5, 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, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 4, 13, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 35, 35, 50, 50, 50, 50, 21, 21, 18, 2, 2, 2, 2, 2, 2, 2, 21, 21, 21, 21, 21, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 21, 19, 21, 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: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358282 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358282/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358282 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 57) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/57 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/57' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2Cc3ncnn3C3(CCN(C(=O)OC(C)(C)C)CC3)C2)cc1) `ZINC001183358282.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183358282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358282/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183358282 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2Cc3ncnn3C3(CCN(C(=O)OC(C)(C)C)CC3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 8, 5, 5, 5, 8, 1, 11, 12, 5, 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, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 3, 3, 1, 1, 1, 1, 4, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 28, 28, 50, 50, 50, 50, 13, 13, 13, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 13, 13, 3, 3] 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: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358282 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183358282 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358282/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358282/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358282 Building ZINC001183358282 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358282' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358282 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183358282 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358282/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358282 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 56) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2Cc3ncnn3C3(CCN(C(=O)OC(C)(C)C)CC3)C2)cc1) `ZINC001183358282.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183358282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183358282 none COc1ccc([C@]([O-])([SiH3])C(=O)N2Cc3ncnn3C3(CCN(C(=O)OC(C)(C)C)CC3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 8, 5, 5, 5, 8, 1, 11, 12, 5, 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, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 4, 13, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 35, 35, 50, 50, 50, 50, 21, 21, 18, 2, 2, 2, 2, 2, 2, 2, 21, 21, 21, 21, 21, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 21, 19, 21, 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: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358282 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358282/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358282 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 57) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2Cc3ncnn3C3(CCN(C(=O)OC(C)(C)C)CC3)C2)cc1) `ZINC001183358282.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183358282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358282/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183358282 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2Cc3ncnn3C3(CCN(C(=O)OC(C)(C)C)CC3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 8, 5, 5, 5, 8, 1, 11, 12, 5, 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, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 3, 3, 1, 1, 1, 1, 4, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 28, 28, 50, 50, 50, 50, 13, 13, 13, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 13, 13, 3, 3] 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: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358282 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183358282 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358282/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358282/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183358282 Building ZINC001183375982 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183375982' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183375982 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183375982 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183375982/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183375982 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 58) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/58 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/58' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](Cc2cnc[nH]2)C(=O)Nc2ccc3c(C)cc(=O)oc3c2)cc1) `ZINC001183375982.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183375982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183375982/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183375982 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](Cc2cnc[nH]2)C(=O)Nc2ccc3c(C)cc(=O)oc3c2)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', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 8, 1, 8, 6, 1, 11, 8, 1, 1, 1, 1, 1, 5, 1, 1, 11, 12, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 9, 10, 10, 10, 10, 10, 4, 8, 8, 8, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 10, 10, 8, 32, 32, 32, 32, 32, 32, 32, 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, 54, 55, 56]) total number of confs: 100 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183375982 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183375982/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183375982 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 59) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/59 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/59' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](Cc2cnc[nH]2)C(=O)Nc2ccc3c(C)cc(=O)oc3c2)cc1) `ZINC001183375982.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183375982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183375982/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183375982 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](Cc2cnc[nH]2)C(=O)Nc2ccc3c(C)cc(=O)oc3c2)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', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 8, 1, 8, 6, 1, 11, 8, 1, 1, 1, 1, 1, 5, 1, 1, 11, 12, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 4, 4, 1, 1, 1, 1, 3, 3, 3, 6, 6, 11, 13, 13, 13, 13, 13, 6, 11, 11, 11, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 4, 4, 4, 4, 4, 4, 4, 3, 11, 11, 13, 13, 11, 32, 32, 32, 32, 32, 32, 32, 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, 54, 55, 56]) total number of confs: 105 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183375982 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183375982 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183375982/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183375982/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183375982 Building ZINC001183375982 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183375982' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183375982 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183375982 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183375982/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183375982 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 58) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/58: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](Cc2cnc[nH]2)C(=O)Nc2ccc3c(C)cc(=O)oc3c2)cc1) `ZINC001183375982.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183375982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183375982/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183375982 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](Cc2cnc[nH]2)C(=O)Nc2ccc3c(C)cc(=O)oc3c2)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', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 8, 1, 8, 6, 1, 11, 8, 1, 1, 1, 1, 1, 5, 1, 1, 11, 12, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 9, 10, 10, 10, 10, 10, 4, 8, 8, 8, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 10, 10, 8, 32, 32, 32, 32, 32, 32, 32, 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, 54, 55, 56]) total number of confs: 100 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183375982 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183375982/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183375982 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 59) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/59: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](Cc2cnc[nH]2)C(=O)Nc2ccc3c(C)cc(=O)oc3c2)cc1) `ZINC001183375982.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183375982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183375982/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183375982 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](Cc2cnc[nH]2)C(=O)Nc2ccc3c(C)cc(=O)oc3c2)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', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 8, 1, 8, 6, 1, 11, 8, 1, 1, 1, 1, 1, 5, 1, 1, 11, 12, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 4, 4, 1, 1, 1, 1, 3, 3, 3, 6, 6, 11, 13, 13, 13, 13, 13, 6, 11, 11, 11, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 4, 4, 4, 4, 4, 4, 4, 3, 11, 11, 13, 13, 11, 32, 32, 32, 32, 32, 32, 32, 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, 54, 55, 56]) total number of confs: 105 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183375982 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183375982 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183375982/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183375982/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183375982 Building ZINC001183377147 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377147' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377147 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183377147 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377147/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377147 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 60) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/60 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/60' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CCCCN)N(C(=O)[C@@]([O-])([SiH3])c1ccc(OC)cc1)S(=O)(=O)c1ccc(C)cc1) `ZINC001183377147.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183377147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001183377147 none COC(=O)[C@H](CCCCN)N(C(=O)[C@@]([O-])([SiH3])c1ccc(OC)cc1)S(=O)(=O)c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.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', 'C.ar', 'S.o2', 'O.2', 'O.2', '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, 12, 1, 11, 5, 7, 5, 5, 5, 5, 10, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 14, 11, 11, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 7, 4, 5, 5, 6, 7, 17, 26, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 4, 7, 7, 7, 10, 10, 10, 10, 10, 10, 7, 7, 7, 6, 6, 7, 7, 17, 17, 26, 26, 26, 26, 2, 2, 4, 4, 4, 2, 2, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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: 163 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377147 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377147/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377147 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 61) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/61 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/61' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CCCCN)N(C(=O)[C@]([O-])([SiH3])c1ccc(OC)cc1)S(=O)(=O)c1ccc(C)cc1) `ZINC001183377147.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183377147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377147/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001183377147 none COC(=O)[C@H](CCCCN)N(C(=O)[C@]([O-])([SiH3])c1ccc(OC)cc1)S(=O)(=O)c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.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', 'C.ar', 'S.o2', 'O.2', 'O.2', '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, 12, 1, 11, 5, 7, 5, 5, 5, 5, 10, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 14, 11, 11, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 6, 3, 4, 4, 5, 7, 11, 17, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 6, 3, 3, 3, 6, 6, 6, 9, 9, 9, 9, 9, 9, 6, 6, 6, 5, 5, 7, 7, 11, 11, 17, 17, 17, 17, 3, 3, 6, 6, 6, 3, 3, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 124 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377147 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183377147 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377147/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377147/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377147 Building ZINC001183377147 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377147' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377147 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183377147 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377147/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377147 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 60) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COC(=O)[C@H](CCCCN)N(C(=O)[C@@]([O-])([SiH3])c1ccc(OC)cc1)S(=O)(=O)c1ccc(C)cc1) `ZINC001183377147.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183377147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001183377147 none COC(=O)[C@H](CCCCN)N(C(=O)[C@@]([O-])([SiH3])c1ccc(OC)cc1)S(=O)(=O)c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.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', 'C.ar', 'S.o2', 'O.2', 'O.2', '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, 12, 1, 11, 5, 7, 5, 5, 5, 5, 10, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 14, 11, 11, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 7, 4, 5, 5, 6, 7, 17, 26, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 4, 7, 7, 7, 10, 10, 10, 10, 10, 10, 7, 7, 7, 6, 6, 7, 7, 17, 17, 26, 26, 26, 26, 2, 2, 4, 4, 4, 2, 2, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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: 163 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377147 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377147/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377147 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 61) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COC(=O)[C@H](CCCCN)N(C(=O)[C@]([O-])([SiH3])c1ccc(OC)cc1)S(=O)(=O)c1ccc(C)cc1) `ZINC001183377147.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183377147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377147/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001183377147 none COC(=O)[C@H](CCCCN)N(C(=O)[C@]([O-])([SiH3])c1ccc(OC)cc1)S(=O)(=O)c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.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', 'C.ar', 'S.o2', 'O.2', 'O.2', '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, 12, 1, 11, 5, 7, 5, 5, 5, 5, 10, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 14, 11, 11, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 6, 3, 4, 4, 5, 7, 11, 17, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 6, 3, 3, 3, 6, 6, 6, 9, 9, 9, 9, 9, 9, 6, 6, 6, 5, 5, 7, 7, 11, 11, 17, 17, 17, 17, 3, 3, 6, 6, 6, 3, 3, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 124 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377147 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183377147 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377147/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377147/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377147 Building ZINC001183377360 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377360' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377360 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183377360 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377360/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377360 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 62) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/62 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/62' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=C[C@@H](OC(CC)CC)[C@@H](NC(C)=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)C1) `ZINC001183377360.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183377360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001183377360 none CCOC(=O)C1=C[C@@H](OC(CC)CC)[C@@H](NC(C)=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 5, 7, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 5, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 6, 21, 6, 6, 6, 6, 6, 7, 7, 7, 7, 11, 6, 6, 6, 7, 7, 7, 2, 6, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 6, 35, 35, 35, 35, 35, 6, 7, 7, 7, 7, 7, 7, 11, 11, 11, 11, 11, 7, 7, 7, 7, 2, 2, 2, 4, 4, 4, 2, 2, 6, 6] 50 rigid atoms, others: [24, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377360 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377360/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377360 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 63) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/63 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/63' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=C[C@@H](OC(CC)CC)[C@@H](NC(C)=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)C1) `ZINC001183377360.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183377360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377360/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001183377360 none CCOC(=O)C1=C[C@@H](OC(CC)CC)[C@@H](NC(C)=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 5, 7, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 5, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 20, 20, 6, 20, 6, 6, 6, 6, 6, 7, 7, 13, 7, 7, 6, 6, 6, 7, 7, 7, 3, 6, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 6, 32, 32, 32, 32, 32, 6, 7, 13, 13, 13, 13, 13, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 2, 2, 4, 4, 4, 2, 2, 6, 6] 50 rigid atoms, others: [24, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377360 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183377360 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377360/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377360/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377360 Building ZINC001183377360 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377360' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377360 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183377360 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377360/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377360 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 62) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCOC(=O)C1=C[C@@H](OC(CC)CC)[C@@H](NC(C)=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)C1) `ZINC001183377360.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183377360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001183377360 none CCOC(=O)C1=C[C@@H](OC(CC)CC)[C@@H](NC(C)=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 5, 7, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 5, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 6, 21, 6, 6, 6, 6, 6, 7, 7, 7, 7, 11, 6, 6, 6, 7, 7, 7, 2, 6, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 6, 35, 35, 35, 35, 35, 6, 7, 7, 7, 7, 7, 7, 11, 11, 11, 11, 11, 7, 7, 7, 7, 2, 2, 2, 4, 4, 4, 2, 2, 6, 6] 50 rigid atoms, others: [24, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377360 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377360/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377360 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 63) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCOC(=O)C1=C[C@@H](OC(CC)CC)[C@@H](NC(C)=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)C1) `ZINC001183377360.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183377360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377360/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001183377360 none CCOC(=O)C1=C[C@@H](OC(CC)CC)[C@@H](NC(C)=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 5, 7, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 5, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 20, 20, 6, 20, 6, 6, 6, 6, 6, 7, 7, 13, 7, 7, 6, 6, 6, 7, 7, 7, 3, 6, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 6, 32, 32, 32, 32, 32, 6, 7, 13, 13, 13, 13, 13, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 2, 2, 4, 4, 4, 2, 2, 6, 6] 50 rigid atoms, others: [24, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377360 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183377360 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377360/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377360/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377360 Building ZINC001183377361 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377361' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377361 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183377361 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377361/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377361 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 64) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/64 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/64' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=C[C@@H](OC(CC)CC)[C@H](NC(C)=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)C1) `ZINC001183377361.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183377361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377361/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001183377361 none CCOC(=O)C1=C[C@@H](OC(CC)CC)[C@H](NC(C)=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 5, 7, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 5, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 18, 18, 8, 18, 8, 8, 8, 8, 8, 10, 10, 12, 10, 14, 8, 8, 8, 11, 11, 11, 3, 8, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 8, 28, 28, 28, 28, 28, 8, 10, 12, 12, 12, 12, 12, 14, 14, 14, 14, 14, 11, 11, 11, 11, 3, 2, 2, 4, 4, 4, 2, 2, 8, 8] 50 rigid atoms, others: [24, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377361 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377361/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377361 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 65) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/65 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/65' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=C[C@@H](OC(CC)CC)[C@H](NC(C)=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)C1) `ZINC001183377361.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183377361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377361/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001183377361 none CCOC(=O)C1=C[C@@H](OC(CC)CC)[C@H](NC(C)=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 5, 7, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 5, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 9, 16, 9, 9, 9, 9, 9, 12, 12, 14, 12, 15, 9, 9, 9, 12, 12, 12, 3, 9, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 9, 28, 28, 28, 28, 28, 9, 12, 14, 14, 14, 14, 14, 15, 15, 15, 15, 15, 12, 12, 12, 12, 3, 2, 2, 4, 4, 4, 2, 2, 9, 9] 50 rigid atoms, others: [24, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377361 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183377361 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377361/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377361/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377361 Building ZINC001183377361 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377361' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377361 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183377361 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377361/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377361 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 64) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCOC(=O)C1=C[C@@H](OC(CC)CC)[C@H](NC(C)=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)C1) `ZINC001183377361.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183377361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377361/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001183377361 none CCOC(=O)C1=C[C@@H](OC(CC)CC)[C@H](NC(C)=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 5, 7, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 5, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 18, 18, 8, 18, 8, 8, 8, 8, 8, 10, 10, 12, 10, 14, 8, 8, 8, 11, 11, 11, 3, 8, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 8, 28, 28, 28, 28, 28, 8, 10, 12, 12, 12, 12, 12, 14, 14, 14, 14, 14, 11, 11, 11, 11, 3, 2, 2, 4, 4, 4, 2, 2, 8, 8] 50 rigid atoms, others: [24, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377361 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377361/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377361 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 65) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCOC(=O)C1=C[C@@H](OC(CC)CC)[C@H](NC(C)=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)C1) `ZINC001183377361.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183377361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377361/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001183377361 none CCOC(=O)C1=C[C@@H](OC(CC)CC)[C@H](NC(C)=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(OC)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 5, 7, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 5, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 9, 16, 9, 9, 9, 9, 9, 12, 12, 14, 12, 15, 9, 9, 9, 12, 12, 12, 3, 9, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 9, 28, 28, 28, 28, 28, 9, 12, 14, 14, 14, 14, 14, 15, 15, 15, 15, 15, 12, 12, 12, 12, 3, 2, 2, 4, 4, 4, 2, 2, 9, 9] 50 rigid atoms, others: [24, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377361 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001183377361 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377361/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377361/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001183377361 Building ZINC001184247783 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247783' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247783 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184247783 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247783/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247783 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 66) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/66 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/66' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2nn(C)c3ncc(I)cc23)ccc1O) `ZINC001184247783.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184247783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247783/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184247783 none COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2nn(C)c3ncc(I)cc23)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', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'I', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 8, 8, 5, 1, 8, 1, 1, 18, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 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, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [18, 7, 7, 7, 4, 1, 1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 7, 7, 7, 18, 18, 18, 7, 4, 4, 3, 14, 14, 14, 14, 14, 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]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247783 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247783/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247783 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 67) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/67 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/67' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2nn(C)c3ncc(I)cc23)ccc1O) `ZINC001184247783.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184247783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247783/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184247783 none COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2nn(C)c3ncc(I)cc23)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', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'I', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 8, 8, 5, 1, 8, 1, 1, 18, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 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, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [18, 8, 8, 8, 5, 1, 1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 8, 8, 18, 18, 18, 8, 5, 5, 3, 14, 14, 14, 14, 14, 8, 8, 16] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247783 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184247783 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247783/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247783/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247783 Building ZINC001184247783 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247783' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247783 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184247783 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247783/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247783 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 66) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2nn(C)c3ncc(I)cc23)ccc1O) `ZINC001184247783.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184247783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247783/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184247783 none COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2nn(C)c3ncc(I)cc23)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', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'I', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 8, 8, 5, 1, 8, 1, 1, 18, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 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, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [18, 7, 7, 7, 4, 1, 1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 7, 7, 7, 18, 18, 18, 7, 4, 4, 3, 14, 14, 14, 14, 14, 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]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247783 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247783/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247783 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 67) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2nn(C)c3ncc(I)cc23)ccc1O) `ZINC001184247783.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184247783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247783/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184247783 none COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2nn(C)c3ncc(I)cc23)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', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'I', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 8, 8, 5, 1, 8, 1, 1, 18, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 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, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [18, 8, 8, 8, 5, 1, 1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 8, 8, 18, 18, 18, 8, 5, 5, 3, 14, 14, 14, 14, 14, 8, 8, 16] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247783 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184247783 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247783/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247783/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247783 Building ZINC001184247784 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247784' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247784 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184247784 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247784/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247784 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 68) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/68 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/68' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2ncnc3c2c(I)cn3C)ccc1O) `ZINC001184247784.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184247784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184247784 none COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2ncnc3c2c(I)cn3C)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', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'I', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 8, 1, 8, 1, 1, 1, 18, 1, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [32, 14, 14, 14, 7, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 14, 14, 14, 14, 32, 32, 32, 14, 7, 7, 3, 10, 10, 10, 10, 10, 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]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247784 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247784/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247784 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 69) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/69 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/69' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2ncnc3c2c(I)cn3C)ccc1O) `ZINC001184247784.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184247784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247784/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184247784 none COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2ncnc3c2c(I)cn3C)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', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'I', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 8, 1, 8, 1, 1, 1, 18, 1, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [32, 14, 14, 14, 7, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 14, 14, 14, 14, 32, 32, 32, 14, 7, 7, 3, 10, 10, 10, 10, 10, 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]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247784 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184247784 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247784/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247784/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247784 Building ZINC001184247784 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247784' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247784 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184247784 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247784/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247784 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 68) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2ncnc3c2c(I)cn3C)ccc1O) `ZINC001184247784.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184247784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184247784 none COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2ncnc3c2c(I)cn3C)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', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'I', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 8, 1, 8, 1, 1, 1, 18, 1, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [32, 14, 14, 14, 7, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 14, 14, 14, 14, 32, 32, 32, 14, 7, 7, 3, 10, 10, 10, 10, 10, 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]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247784 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247784/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247784 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 69) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2ncnc3c2c(I)cn3C)ccc1O) `ZINC001184247784.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184247784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247784/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184247784 none COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2ncnc3c2c(I)cn3C)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', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'I', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 8, 1, 8, 1, 1, 1, 18, 1, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [32, 14, 14, 14, 7, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 14, 14, 14, 14, 32, 32, 32, 14, 7, 7, 3, 10, 10, 10, 10, 10, 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]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247784 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184247784 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247784/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247784/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247784 Building ZINC001184247843 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247843' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247843 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184247843 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247843/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247843 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 70) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/70 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/70' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2cc(I)c3nccn3c2)ccc1O) `ZINC001184247843.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184247843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184247843 none COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2cc(I)c3nccn3c2)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', 'C.2', 'I', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', '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, 1, 18, 1, 8, 1, 1, 8, 1, 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, 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: [15, 6, 6, 6, 3, 1, 1, 1, 1, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 6, 15, 15, 15, 6, 3, 3, 3, 15, 15, 15, 15, 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]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247843 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247843/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247843 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 71) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/71 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/71' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2cc(I)c3nccn3c2)ccc1O) `ZINC001184247843.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184247843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247843/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184247843 none COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2cc(I)c3nccn3c2)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', 'C.2', 'I', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', '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, 1, 18, 1, 8, 1, 1, 8, 1, 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, 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: [15, 6, 6, 6, 3, 1, 1, 1, 1, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 6, 15, 15, 15, 6, 3, 3, 3, 15, 15, 15, 15, 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]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247843 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184247843 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247843/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247843/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247843 Building ZINC001184247843 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247843' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247843 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184247843 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247843/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247843 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 70) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2cc(I)c3nccn3c2)ccc1O) `ZINC001184247843.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184247843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184247843 none COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2cc(I)c3nccn3c2)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', 'C.2', 'I', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', '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, 1, 18, 1, 8, 1, 1, 8, 1, 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, 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: [15, 6, 6, 6, 3, 1, 1, 1, 1, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 6, 15, 15, 15, 6, 3, 3, 3, 15, 15, 15, 15, 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]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247843 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247843/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247843 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 71) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2cc(I)c3nccn3c2)ccc1O) `ZINC001184247843.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184247843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247843/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184247843 none COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2cc(I)c3nccn3c2)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', 'C.2', 'I', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', '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, 1, 18, 1, 8, 1, 1, 8, 1, 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, 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: [15, 6, 6, 6, 3, 1, 1, 1, 1, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 6, 15, 15, 15, 6, 3, 3, 3, 15, 15, 15, 15, 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]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247843 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184247843 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247843/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247843/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247843 Building ZINC001184247903 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247903' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247903 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184247903 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247903/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247903 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 72) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/72 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/72' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@@]3(C2)CCC[C@H](CNC(=O)c2ccccc2)O3)ccc1O) `ZINC001184247903.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184247903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184247903 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@@]3(C2)CCC[C@H](CNC(=O)c2ccccc2)O3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 12, 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, 6] 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [14, 10, 10, 10, 5, 1, 1, 1, 1, 3, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 29, 29, 29, 32, 32, 32, 32, 32, 6, 10, 10, 10, 10, 14, 14, 14, 10, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 29, 32, 32, 32, 32, 32, 10, 10, 20] 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, 60, 61, 62, 63]) total number of confs: 154 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247903 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247903/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247903 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 73) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/73 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/73' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@@]3(C2)CCC[C@H](CNC(=O)c2ccccc2)O3)ccc1O) `ZINC001184247903.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184247903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247903/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184247903 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@@]3(C2)CCC[C@H](CNC(=O)c2ccccc2)O3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 12, 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, 6] 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 7, 7, 7, 4, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 20, 20, 20, 26, 26, 26, 26, 26, 4, 7, 7, 7, 7, 12, 12, 12, 7, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 20, 26, 26, 26, 26, 26, 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, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247903 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184247903 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247903/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247903/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247903 Building ZINC001184247903 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247903' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247903 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184247903 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247903/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247903 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 72) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@@]3(C2)CCC[C@H](CNC(=O)c2ccccc2)O3)ccc1O) `ZINC001184247903.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184247903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184247903 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@@]3(C2)CCC[C@H](CNC(=O)c2ccccc2)O3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 12, 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, 6] 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [14, 10, 10, 10, 5, 1, 1, 1, 1, 3, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 29, 29, 29, 32, 32, 32, 32, 32, 6, 10, 10, 10, 10, 14, 14, 14, 10, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 29, 32, 32, 32, 32, 32, 10, 10, 20] 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, 60, 61, 62, 63]) total number of confs: 154 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247903 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247903/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247903 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 73) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@@]3(C2)CCC[C@H](CNC(=O)c2ccccc2)O3)ccc1O) `ZINC001184247903.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184247903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247903/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184247903 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@@]3(C2)CCC[C@H](CNC(=O)c2ccccc2)O3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 12, 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, 6] 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 7, 7, 7, 4, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 20, 20, 20, 26, 26, 26, 26, 26, 4, 7, 7, 7, 7, 12, 12, 12, 7, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 20, 26, 26, 26, 26, 26, 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, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247903 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184247903 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247903/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247903/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247903 Building ZINC001184247971 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247971' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247971 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184247971 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247971/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247971 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 74) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/74 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/74' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@@]3(CCN(Cc4csc(C)n4)C3=O)C2)ccc1O) `ZINC001184247971.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184247971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184247971 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@@]3(CCN(Cc4csc(C)n4)C3=O)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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 5, 1, 1, 14, 1, 5, 8, 1, 11, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 12, 28, 28, 28, 28, 28, 2, 2, 2, 6, 6, 6, 6, 9, 9, 9, 6, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 28, 28, 28, 28, 2, 2, 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, 55, 56, 57, 58]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247971 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247971/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247971 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 75) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/75 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/75' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@@]3(CCN(Cc4csc(C)n4)C3=O)C2)ccc1O) `ZINC001184247971.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184247971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247971/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184247971 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@@]3(CCN(Cc4csc(C)n4)C3=O)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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 5, 1, 1, 14, 1, 5, 8, 1, 11, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [19, 9, 9, 9, 5, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10, 22, 22, 22, 22, 22, 2, 2, 2, 9, 9, 9, 9, 19, 19, 19, 9, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 22, 22, 22, 22, 2, 2, 9, 9, 18] 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]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247971 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184247971 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247971/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247971/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247971 Building ZINC001184247971 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247971' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247971 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184247971 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247971/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247971 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 74) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@@]3(CCN(Cc4csc(C)n4)C3=O)C2)ccc1O) `ZINC001184247971.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184247971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184247971 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@@]3(CCN(Cc4csc(C)n4)C3=O)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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 5, 1, 1, 14, 1, 5, 8, 1, 11, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 12, 28, 28, 28, 28, 28, 2, 2, 2, 6, 6, 6, 6, 9, 9, 9, 6, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 28, 28, 28, 28, 2, 2, 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, 55, 56, 57, 58]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247971 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247971/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247971 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 75) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@@]3(CCN(Cc4csc(C)n4)C3=O)C2)ccc1O) `ZINC001184247971.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184247971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247971/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184247971 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@@]3(CCN(Cc4csc(C)n4)C3=O)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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 5, 1, 1, 14, 1, 5, 8, 1, 11, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [19, 9, 9, 9, 5, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10, 22, 22, 22, 22, 22, 2, 2, 2, 9, 9, 9, 9, 19, 19, 19, 9, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 22, 22, 22, 22, 2, 2, 9, 9, 18] 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]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247971 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184247971 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247971/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247971/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247971 Building ZINC001184247975 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247975' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247975 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184247975 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247975/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247975 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 76) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/76 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/76' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@]3(CCN(Cc4csc(C)n4)C3=O)C2)ccc1O) `ZINC001184247975.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184247975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184247975 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@]3(CCN(Cc4csc(C)n4)C3=O)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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 5, 1, 1, 14, 1, 5, 8, 1, 11, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 3, 3, 3, 3, 3, 14, 25, 25, 25, 25, 25, 3, 3, 3, 11, 11, 11, 11, 20, 20, 20, 11, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 25, 25, 25, 25, 3, 3, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 133 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247975 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247975/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247975 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 77) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/77 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/77' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@]3(CCN(Cc4csc(C)n4)C3=O)C2)ccc1O) `ZINC001184247975.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184247975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247975/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184247975 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@]3(CCN(Cc4csc(C)n4)C3=O)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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 5, 1, 1, 14, 1, 5, 8, 1, 11, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [14, 7, 7, 7, 4, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 25, 25, 25, 25, 25, 3, 3, 3, 7, 7, 7, 7, 14, 14, 14, 7, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 25, 25, 25, 25, 3, 3, 7, 7, 14] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247975 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184247975 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247975/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247975/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247975 Building ZINC001184247975 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247975' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247975 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184247975 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247975/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247975 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 76) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@]3(CCN(Cc4csc(C)n4)C3=O)C2)ccc1O) `ZINC001184247975.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184247975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184247975 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@]3(CCN(Cc4csc(C)n4)C3=O)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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 5, 1, 1, 14, 1, 5, 8, 1, 11, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 3, 3, 3, 3, 3, 14, 25, 25, 25, 25, 25, 3, 3, 3, 11, 11, 11, 11, 20, 20, 20, 11, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 25, 25, 25, 25, 3, 3, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 133 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247975 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247975/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247975 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 77) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@]3(CCN(Cc4csc(C)n4)C3=O)C2)ccc1O) `ZINC001184247975.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184247975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247975/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184247975 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@]3(CCN(Cc4csc(C)n4)C3=O)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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 5, 1, 1, 14, 1, 5, 8, 1, 11, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [14, 7, 7, 7, 4, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 25, 25, 25, 25, 25, 3, 3, 3, 7, 7, 7, 7, 14, 14, 14, 7, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 25, 25, 25, 25, 3, 3, 7, 7, 14] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247975 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184247975 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247975/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247975/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247975 Building ZINC001184247989 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247989' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247989 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184247989 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247989/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247989 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 78) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/78 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/78' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@H]3OCC[C@@H](C(=O)Nc4cccnc4C)[C@H]3C2)ccc1O) `ZINC001184247989.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184247989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184247989 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@H]3OCC[C@@H](C(=O)Nc4cccnc4C)[C@H]3C2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 1, 1, 1, 12, 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, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 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, 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: [23, 10, 10, 10, 6, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 17, 17, 17, 17, 17, 17, 4, 4, 4, 10, 10, 10, 10, 23, 23, 23, 10, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 10, 17, 17, 17, 17, 17, 17, 4, 4, 10, 10, 20] 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, 60, 61, 62]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247989 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247989/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247989 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 79) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/79 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/79' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@H]3OCC[C@@H](C(=O)Nc4cccnc4C)[C@H]3C2)ccc1O) `ZINC001184247989.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184247989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247989/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184247989 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@H]3OCC[C@@H](C(=O)Nc4cccnc4C)[C@H]3C2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 1, 1, 1, 12, 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, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [25, 12, 12, 12, 7, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 22, 22, 22, 22, 22, 22, 3, 3, 3, 12, 12, 12, 12, 25, 25, 25, 12, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 11, 22, 22, 22, 22, 22, 22, 3, 3, 12, 12, 24] 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, 60, 61, 62]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247989 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184247989 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247989/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247989/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247989 Building ZINC001184247989 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247989' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247989 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184247989 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247989/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247989 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 78) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@H]3OCC[C@@H](C(=O)Nc4cccnc4C)[C@H]3C2)ccc1O) `ZINC001184247989.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184247989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184247989 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@H]3OCC[C@@H](C(=O)Nc4cccnc4C)[C@H]3C2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 1, 1, 1, 12, 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, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 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, 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: [23, 10, 10, 10, 6, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 17, 17, 17, 17, 17, 17, 4, 4, 4, 10, 10, 10, 10, 23, 23, 23, 10, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 10, 17, 17, 17, 17, 17, 17, 4, 4, 10, 10, 20] 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, 60, 61, 62]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247989 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247989/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247989 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 79) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@H]3OCC[C@@H](C(=O)Nc4cccnc4C)[C@H]3C2)ccc1O) `ZINC001184247989.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184247989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247989/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184247989 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@H]3OCC[C@@H](C(=O)Nc4cccnc4C)[C@H]3C2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 1, 5, 5, 7, 5, 1, 1, 1, 12, 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, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [25, 12, 12, 12, 7, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 22, 22, 22, 22, 22, 22, 3, 3, 3, 12, 12, 12, 12, 25, 25, 25, 12, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 11, 22, 22, 22, 22, 22, 22, 3, 3, 12, 12, 24] 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, 60, 61, 62]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247989 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184247989 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247989/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247989/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184247989 Building ZINC001184248303 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184248303 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 80) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/80 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/80' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2) `ZINC001184248303.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184248303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184248303 none COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 8, 4, 4, 4, 4, 4, 4, 4, 4, 10, 18, 18, 18, 18, 18, 4, 4, 2, 1, 2, 1, 1, 1, 4, 8, 8, 8, 8, 8, 8, 13, 8, 4, 4, 12, 12, 12, 8, 8, 4, 4, 4, 4, 10, 10, 18, 18, 18, 18, 4, 4, 4, 4, 4, 4, 8, 8, 16, 13, 13, 13, 8, 4, 4, 4, 4] 100 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, 62, 63, 64, 65, 66]) total number of confs: 131 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 81) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/81 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/81' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2) `ZINC001184248303.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184248303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184248303 none COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [15, 11, 5, 5, 5, 5, 5, 5, 5, 5, 12, 18, 18, 18, 18, 18, 5, 4, 2, 1, 2, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 14, 6, 5, 5, 15, 15, 15, 11, 11, 5, 5, 5, 5, 12, 12, 18, 18, 18, 18, 5, 5, 5, 5, 3, 3, 6, 6, 12, 14, 14, 14, 6, 5, 5, 5, 5] 100 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, 62, 63, 64, 65, 66]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 82) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/82 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/82' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2) `ZINC001184248303.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184248303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184248303 none COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 8, 4, 4, 4, 4, 4, 4, 4, 4, 10, 18, 18, 18, 18, 18, 4, 4, 2, 1, 2, 1, 1, 1, 4, 8, 8, 8, 8, 8, 8, 13, 8, 4, 4, 12, 12, 12, 8, 8, 4, 4, 4, 4, 10, 10, 18, 18, 18, 18, 4, 4, 4, 4, 4, 4, 8, 8, 16, 13, 13, 13, 8, 4, 4, 4, 4] 100 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, 62, 63, 64, 65, 66]) total number of confs: 131 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 83) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/83 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/83' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2) `ZINC001184248303.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184248303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184248303 none COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [15, 11, 5, 5, 5, 5, 5, 5, 5, 5, 12, 18, 18, 18, 18, 18, 5, 4, 2, 1, 2, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 14, 6, 5, 5, 15, 15, 15, 11, 11, 5, 5, 5, 5, 12, 12, 18, 18, 18, 18, 5, 5, 5, 5, 3, 3, 6, 6, 12, 14, 14, 14, 6, 5, 5, 5, 5] 100 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, 62, 63, 64, 65, 66]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184248303 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303 Building ZINC001184248303 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184248303 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 80) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2) `ZINC001184248303.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184248303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184248303 none COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 8, 4, 4, 4, 4, 4, 4, 4, 4, 10, 18, 18, 18, 18, 18, 4, 4, 2, 1, 2, 1, 1, 1, 4, 8, 8, 8, 8, 8, 8, 13, 8, 4, 4, 12, 12, 12, 8, 8, 4, 4, 4, 4, 10, 10, 18, 18, 18, 18, 4, 4, 4, 4, 4, 4, 8, 8, 16, 13, 13, 13, 8, 4, 4, 4, 4] 100 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, 62, 63, 64, 65, 66]) total number of confs: 131 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 81) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2) `ZINC001184248303.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184248303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184248303 none COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [15, 11, 5, 5, 5, 5, 5, 5, 5, 5, 12, 18, 18, 18, 18, 18, 5, 4, 2, 1, 2, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 14, 6, 5, 5, 15, 15, 15, 11, 11, 5, 5, 5, 5, 12, 12, 18, 18, 18, 18, 5, 5, 5, 5, 3, 3, 6, 6, 12, 14, 14, 14, 6, 5, 5, 5, 5] 100 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, 62, 63, 64, 65, 66]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 82) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/82: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2) `ZINC001184248303.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184248303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184248303 none COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 8, 4, 4, 4, 4, 4, 4, 4, 4, 10, 18, 18, 18, 18, 18, 4, 4, 2, 1, 2, 1, 1, 1, 4, 8, 8, 8, 8, 8, 8, 13, 8, 4, 4, 12, 12, 12, 8, 8, 4, 4, 4, 4, 10, 10, 18, 18, 18, 18, 4, 4, 4, 4, 4, 4, 8, 8, 16, 13, 13, 13, 8, 4, 4, 4, 4] 100 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, 62, 63, 64, 65, 66]) total number of confs: 131 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 83) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/83: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2) `ZINC001184248303.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184248303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184248303 none COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [15, 11, 5, 5, 5, 5, 5, 5, 5, 5, 12, 18, 18, 18, 18, 18, 5, 4, 2, 1, 2, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 14, 6, 5, 5, 15, 15, 15, 11, 11, 5, 5, 5, 5, 12, 12, 18, 18, 18, 18, 5, 5, 5, 5, 3, 3, 6, 6, 12, 14, 14, 14, 6, 5, 5, 5, 5] 100 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, 62, 63, 64, 65, 66]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184248303 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303 Building ZINC001184248303 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184248303 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 80) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2) `ZINC001184248303.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184248303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184248303 none COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 8, 4, 4, 4, 4, 4, 4, 4, 4, 10, 18, 18, 18, 18, 18, 4, 4, 2, 1, 2, 1, 1, 1, 4, 8, 8, 8, 8, 8, 8, 13, 8, 4, 4, 12, 12, 12, 8, 8, 4, 4, 4, 4, 10, 10, 18, 18, 18, 18, 4, 4, 4, 4, 4, 4, 8, 8, 16, 13, 13, 13, 8, 4, 4, 4, 4] 100 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, 62, 63, 64, 65, 66]) total number of confs: 131 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 81) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2) `ZINC001184248303.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184248303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184248303 none COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [15, 11, 5, 5, 5, 5, 5, 5, 5, 5, 12, 18, 18, 18, 18, 18, 5, 4, 2, 1, 2, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 14, 6, 5, 5, 15, 15, 15, 11, 11, 5, 5, 5, 5, 12, 12, 18, 18, 18, 18, 5, 5, 5, 5, 3, 3, 6, 6, 12, 14, 14, 14, 6, 5, 5, 5, 5] 100 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, 62, 63, 64, 65, 66]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 82) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/82: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2) `ZINC001184248303.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184248303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184248303 none COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 8, 4, 4, 4, 4, 4, 4, 4, 4, 10, 18, 18, 18, 18, 18, 4, 4, 2, 1, 2, 1, 1, 1, 4, 8, 8, 8, 8, 8, 8, 13, 8, 4, 4, 12, 12, 12, 8, 8, 4, 4, 4, 4, 10, 10, 18, 18, 18, 18, 4, 4, 4, 4, 4, 4, 8, 8, 16, 13, 13, 13, 8, 4, 4, 4, 4] 100 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, 62, 63, 64, 65, 66]) total number of confs: 131 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 83) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/83: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2) `ZINC001184248303.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184248303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184248303 none COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [15, 11, 5, 5, 5, 5, 5, 5, 5, 5, 12, 18, 18, 18, 18, 18, 5, 4, 2, 1, 2, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 14, 6, 5, 5, 15, 15, 15, 11, 11, 5, 5, 5, 5, 12, 12, 18, 18, 18, 18, 5, 5, 5, 5, 3, 3, 6, 6, 12, 14, 14, 14, 6, 5, 5, 5, 5] 100 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, 62, 63, 64, 65, 66]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184248303 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303 Building ZINC001184248303 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184248303 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 80) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2) `ZINC001184248303.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184248303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184248303 none COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 8, 4, 4, 4, 4, 4, 4, 4, 4, 10, 18, 18, 18, 18, 18, 4, 4, 2, 1, 2, 1, 1, 1, 4, 8, 8, 8, 8, 8, 8, 13, 8, 4, 4, 12, 12, 12, 8, 8, 4, 4, 4, 4, 10, 10, 18, 18, 18, 18, 4, 4, 4, 4, 4, 4, 8, 8, 16, 13, 13, 13, 8, 4, 4, 4, 4] 100 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, 62, 63, 64, 65, 66]) total number of confs: 131 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 81) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2) `ZINC001184248303.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184248303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184248303 none COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [15, 11, 5, 5, 5, 5, 5, 5, 5, 5, 12, 18, 18, 18, 18, 18, 5, 4, 2, 1, 2, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 14, 6, 5, 5, 15, 15, 15, 11, 11, 5, 5, 5, 5, 12, 12, 18, 18, 18, 18, 5, 5, 5, 5, 3, 3, 6, 6, 12, 14, 14, 14, 6, 5, 5, 5, 5] 100 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, 62, 63, 64, 65, 66]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 82) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/82: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2) `ZINC001184248303.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184248303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184248303 none COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 8, 4, 4, 4, 4, 4, 4, 4, 4, 10, 18, 18, 18, 18, 18, 4, 4, 2, 1, 2, 1, 1, 1, 4, 8, 8, 8, 8, 8, 8, 13, 8, 4, 4, 12, 12, 12, 8, 8, 4, 4, 4, 4, 10, 10, 18, 18, 18, 18, 4, 4, 4, 4, 4, 4, 8, 8, 16, 13, 13, 13, 8, 4, 4, 4, 4] 100 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, 62, 63, 64, 65, 66]) total number of confs: 131 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 83) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/83: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2) `ZINC001184248303.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184248303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184248303 none COC[C@@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [15, 11, 5, 5, 5, 5, 5, 5, 5, 5, 12, 18, 18, 18, 18, 18, 5, 4, 2, 1, 2, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 14, 6, 5, 5, 15, 15, 15, 11, 11, 5, 5, 5, 5, 12, 12, 18, 18, 18, 18, 5, 5, 5, 5, 3, 3, 6, 6, 12, 14, 14, 14, 6, 5, 5, 5, 5] 100 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, 62, 63, 64, 65, 66]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184248303 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248303 Building ZINC001184248304 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184248304 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 84) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/84 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/84' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2) `ZINC001184248304.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184248304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184248304 none COC[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [14, 8, 3, 3, 3, 3, 3, 3, 3, 3, 7, 11, 11, 11, 11, 11, 3, 3, 2, 1, 3, 1, 1, 1, 5, 10, 10, 10, 10, 10, 10, 19, 10, 3, 3, 14, 14, 14, 8, 8, 3, 3, 3, 3, 7, 7, 11, 11, 11, 11, 3, 3, 3, 3, 5, 5, 10, 10, 20, 19, 19, 19, 10, 3, 3, 3, 3] 100 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, 62, 63, 64, 65, 66]) total number of confs: 130 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 85) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/85 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/85' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2) `ZINC001184248304.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184248304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184248304 none COC[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 14, 5, 5, 5, 5, 5, 5, 5, 5, 11, 17, 17, 17, 17, 17, 5, 5, 3, 1, 5, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 16, 9, 5, 5, 16, 16, 16, 14, 14, 5, 5, 5, 5, 11, 11, 17, 17, 17, 17, 5, 5, 5, 5, 5, 5, 9, 9, 18, 16, 16, 16, 9, 5, 5, 5, 5] 100 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, 62, 63, 64, 65, 66]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 86) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/86 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/86' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2) `ZINC001184248304.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184248304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184248304 none COC[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [14, 8, 3, 3, 3, 3, 3, 3, 3, 3, 7, 11, 11, 11, 11, 11, 3, 3, 2, 1, 3, 1, 1, 1, 5, 10, 10, 10, 10, 10, 10, 19, 10, 3, 3, 14, 14, 14, 8, 8, 3, 3, 3, 3, 7, 7, 11, 11, 11, 11, 3, 3, 3, 3, 5, 5, 10, 10, 20, 19, 19, 19, 10, 3, 3, 3, 3] 100 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, 62, 63, 64, 65, 66]) total number of confs: 130 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 87) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/87 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/87' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2) `ZINC001184248304.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184248304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184248304 none COC[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 14, 5, 5, 5, 5, 5, 5, 5, 5, 11, 17, 17, 17, 17, 17, 5, 5, 3, 1, 5, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 16, 9, 5, 5, 16, 16, 16, 14, 14, 5, 5, 5, 5, 11, 11, 17, 17, 17, 17, 5, 5, 5, 5, 5, 5, 9, 9, 18, 16, 16, 16, 9, 5, 5, 5, 5] 100 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, 62, 63, 64, 65, 66]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184248304 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304 Building ZINC001184248304 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184248304 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 84) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COC[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2) `ZINC001184248304.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184248304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184248304 none COC[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [14, 8, 3, 3, 3, 3, 3, 3, 3, 3, 7, 11, 11, 11, 11, 11, 3, 3, 2, 1, 3, 1, 1, 1, 5, 10, 10, 10, 10, 10, 10, 19, 10, 3, 3, 14, 14, 14, 8, 8, 3, 3, 3, 3, 7, 7, 11, 11, 11, 11, 3, 3, 3, 3, 5, 5, 10, 10, 20, 19, 19, 19, 10, 3, 3, 3, 3] 100 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, 62, 63, 64, 65, 66]) total number of confs: 130 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 85) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COC[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2) `ZINC001184248304.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184248304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184248304 none COC[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 14, 5, 5, 5, 5, 5, 5, 5, 5, 11, 17, 17, 17, 17, 17, 5, 5, 3, 1, 5, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 16, 9, 5, 5, 16, 16, 16, 14, 14, 5, 5, 5, 5, 11, 11, 17, 17, 17, 17, 5, 5, 5, 5, 5, 5, 9, 9, 18, 16, 16, 16, 9, 5, 5, 5, 5] 100 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, 62, 63, 64, 65, 66]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 86) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/86: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2) `ZINC001184248304.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184248304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184248304 none COC[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [14, 8, 3, 3, 3, 3, 3, 3, 3, 3, 7, 11, 11, 11, 11, 11, 3, 3, 2, 1, 3, 1, 1, 1, 5, 10, 10, 10, 10, 10, 10, 19, 10, 3, 3, 14, 14, 14, 8, 8, 3, 3, 3, 3, 7, 7, 11, 11, 11, 11, 3, 3, 3, 3, 5, 5, 10, 10, 20, 19, 19, 19, 10, 3, 3, 3, 3] 100 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, 62, 63, 64, 65, 66]) total number of confs: 130 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 87) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/87: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2) `ZINC001184248304.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184248304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184248304 none COC[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 14, 5, 5, 5, 5, 5, 5, 5, 5, 11, 17, 17, 17, 17, 17, 5, 5, 3, 1, 5, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 16, 9, 5, 5, 16, 16, 16, 14, 14, 5, 5, 5, 5, 11, 11, 17, 17, 17, 17, 5, 5, 5, 5, 5, 5, 9, 9, 18, 16, 16, 16, 9, 5, 5, 5, 5] 100 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, 62, 63, 64, 65, 66]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184248304 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304 Building ZINC001184248304 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184248304 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 84) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COC[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2) `ZINC001184248304.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184248304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184248304 none COC[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [14, 8, 3, 3, 3, 3, 3, 3, 3, 3, 7, 11, 11, 11, 11, 11, 3, 3, 2, 1, 3, 1, 1, 1, 5, 10, 10, 10, 10, 10, 10, 19, 10, 3, 3, 14, 14, 14, 8, 8, 3, 3, 3, 3, 7, 7, 11, 11, 11, 11, 3, 3, 3, 3, 5, 5, 10, 10, 20, 19, 19, 19, 10, 3, 3, 3, 3] 100 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, 62, 63, 64, 65, 66]) total number of confs: 130 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 85) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COC[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2) `ZINC001184248304.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184248304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184248304 none COC[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 14, 5, 5, 5, 5, 5, 5, 5, 5, 11, 17, 17, 17, 17, 17, 5, 5, 3, 1, 5, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 16, 9, 5, 5, 16, 16, 16, 14, 14, 5, 5, 5, 5, 11, 11, 17, 17, 17, 17, 5, 5, 5, 5, 5, 5, 9, 9, 18, 16, 16, 16, 9, 5, 5, 5, 5] 100 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, 62, 63, 64, 65, 66]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 86) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/86: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2) `ZINC001184248304.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184248304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184248304 none COC[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [14, 8, 3, 3, 3, 3, 3, 3, 3, 3, 7, 11, 11, 11, 11, 11, 3, 3, 2, 1, 3, 1, 1, 1, 5, 10, 10, 10, 10, 10, 10, 19, 10, 3, 3, 14, 14, 14, 8, 8, 3, 3, 3, 3, 7, 7, 11, 11, 11, 11, 3, 3, 3, 3, 5, 5, 10, 10, 20, 19, 19, 19, 10, 3, 3, 3, 3] 100 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, 62, 63, 64, 65, 66]) total number of confs: 130 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 87) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/87: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2) `ZINC001184248304.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184248304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184248304 none COC[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 14, 5, 5, 5, 5, 5, 5, 5, 5, 11, 17, 17, 17, 17, 17, 5, 5, 3, 1, 5, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 16, 9, 5, 5, 16, 16, 16, 14, 14, 5, 5, 5, 5, 11, 11, 17, 17, 17, 17, 5, 5, 5, 5, 5, 5, 9, 9, 18, 16, 16, 16, 9, 5, 5, 5, 5] 100 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, 62, 63, 64, 65, 66]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184248304 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304 Building ZINC001184248304 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184248304 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 84) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COC[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2) `ZINC001184248304.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184248304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184248304 none COC[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [14, 8, 3, 3, 3, 3, 3, 3, 3, 3, 7, 11, 11, 11, 11, 11, 3, 3, 2, 1, 3, 1, 1, 1, 5, 10, 10, 10, 10, 10, 10, 19, 10, 3, 3, 14, 14, 14, 8, 8, 3, 3, 3, 3, 7, 7, 11, 11, 11, 11, 3, 3, 3, 3, 5, 5, 10, 10, 20, 19, 19, 19, 10, 3, 3, 3, 3] 100 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, 62, 63, 64, 65, 66]) total number of confs: 130 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 85) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COC[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2) `ZINC001184248304.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184248304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184248304 none COC[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 14, 5, 5, 5, 5, 5, 5, 5, 5, 11, 17, 17, 17, 17, 17, 5, 5, 3, 1, 5, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 16, 9, 5, 5, 16, 16, 16, 14, 14, 5, 5, 5, 5, 11, 11, 17, 17, 17, 17, 5, 5, 5, 5, 5, 5, 9, 9, 18, 16, 16, 16, 9, 5, 5, 5, 5] 100 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, 62, 63, 64, 65, 66]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 86) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/86: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2) `ZINC001184248304.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184248304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184248304 none COC[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [14, 8, 3, 3, 3, 3, 3, 3, 3, 3, 7, 11, 11, 11, 11, 11, 3, 3, 2, 1, 3, 1, 1, 1, 5, 10, 10, 10, 10, 10, 10, 19, 10, 3, 3, 14, 14, 14, 8, 8, 3, 3, 3, 3, 7, 7, 11, 11, 11, 11, 3, 3, 3, 3, 5, 5, 10, 10, 20, 19, 19, 19, 10, 3, 3, 3, 3] 100 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, 62, 63, 64, 65, 66]) total number of confs: 130 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 87) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/87: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2) `ZINC001184248304.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184248304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184248304 none COC[C@H]1CC2(CN1Cc1ccccn1)CCN(C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 14, 5, 5, 5, 5, 5, 5, 5, 5, 11, 17, 17, 17, 17, 17, 5, 5, 3, 1, 5, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 16, 9, 5, 5, 16, 16, 16, 14, 14, 5, 5, 5, 5, 11, 11, 17, 17, 17, 17, 5, 5, 5, 5, 5, 5, 9, 9, 18, 16, 16, 16, 9, 5, 5, 5, 5] 100 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, 62, 63, 64, 65, 66]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184248304 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248304 Building ZINC001184248325 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248325' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248325 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184248325 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248325/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248325 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 88) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/88 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/88' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@@]34CN(C(=O)OC(C)(C)C)C[C@@H](C[C@@H]3C2)O4)ccc1O) `ZINC001184248325.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184248325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184248325 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@@]34CN(C(=O)OC(C)(C)C)C[C@@H](C[C@@H]3C2)O4)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 7, 5, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 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, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 9, 9, 9, 5, 1, 1, 1, 2, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 16, 17, 17, 17, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 13, 13, 13, 9, 5, 5, 6, 6, 6, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 6, 6, 6, 6, 9, 9, 18] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248325 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248325/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248325 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 89) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/89 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/89' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@@]34CN(C(=O)OC(C)(C)C)C[C@@H](C[C@@H]3C2)O4)ccc1O) `ZINC001184248325.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184248325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248325/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184248325 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@@]34CN(C(=O)OC(C)(C)C)C[C@@H](C[C@@H]3C2)O4)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 7, 5, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 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, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [14, 10, 10, 10, 5, 1, 1, 1, 2, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 19, 20, 20, 20, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 10, 14, 14, 14, 10, 5, 5, 6, 6, 6, 6, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 6, 6, 6, 10, 10, 20] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 107 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248325 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184248325 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248325/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248325/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248325 Building ZINC001184248325 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248325' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248325 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184248325 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248325/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248325 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 88) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@@]34CN(C(=O)OC(C)(C)C)C[C@@H](C[C@@H]3C2)O4)ccc1O) `ZINC001184248325.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184248325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184248325 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@@]34CN(C(=O)OC(C)(C)C)C[C@@H](C[C@@H]3C2)O4)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 7, 5, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 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, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 9, 9, 9, 5, 1, 1, 1, 2, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 16, 17, 17, 17, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 13, 13, 13, 9, 5, 5, 6, 6, 6, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 6, 6, 6, 6, 9, 9, 18] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248325 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248325/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248325 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 89) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@@]34CN(C(=O)OC(C)(C)C)C[C@@H](C[C@@H]3C2)O4)ccc1O) `ZINC001184248325.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184248325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248325/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184248325 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@@]34CN(C(=O)OC(C)(C)C)C[C@@H](C[C@@H]3C2)O4)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 7, 5, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 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, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [14, 10, 10, 10, 5, 1, 1, 1, 2, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 19, 20, 20, 20, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 10, 14, 14, 14, 10, 5, 5, 6, 6, 6, 6, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 6, 6, 6, 10, 10, 20] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 107 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248325 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184248325 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248325/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248325/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248325 Building ZINC001184248326 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248326' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248326 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184248326 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248326/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248326 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 90) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/90 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/90' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@@]34CN(C(=O)OC(C)(C)C)C[C@@H](C[C@H]3C2)O4)ccc1O) `ZINC001184248326.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184248326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248326/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184248326 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@@]34CN(C(=O)OC(C)(C)C)C[C@@H](C[C@H]3C2)O4)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 7, 5, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 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, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [19, 10, 10, 10, 5, 1, 1, 1, 2, 6, 6, 6, 6, 6, 6, 6, 6, 16, 16, 20, 21, 21, 21, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 10, 19, 19, 19, 10, 5, 5, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 6, 6, 10, 10, 20] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 118 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248326 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248326/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248326 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 91) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/91 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/91' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@@]34CN(C(=O)OC(C)(C)C)C[C@@H](C[C@H]3C2)O4)ccc1O) `ZINC001184248326.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184248326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248326/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184248326 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@@]34CN(C(=O)OC(C)(C)C)C[C@@H](C[C@H]3C2)O4)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 7, 5, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 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, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [19, 11, 11, 11, 6, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 22, 24, 24, 24, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 19, 19, 19, 11, 6, 6, 4, 4, 4, 4, 4, 4, 24, 24, 24, 24, 24, 24, 24, 24, 24, 4, 4, 4, 4, 4, 4, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 118 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248326 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184248326 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248326/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248326/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248326 Building ZINC001184248326 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248326' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248326 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184248326 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248326/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248326 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 90) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@@]34CN(C(=O)OC(C)(C)C)C[C@@H](C[C@H]3C2)O4)ccc1O) `ZINC001184248326.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184248326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248326/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184248326 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@@]34CN(C(=O)OC(C)(C)C)C[C@@H](C[C@H]3C2)O4)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 7, 5, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 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, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [19, 10, 10, 10, 5, 1, 1, 1, 2, 6, 6, 6, 6, 6, 6, 6, 6, 16, 16, 20, 21, 21, 21, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 10, 19, 19, 19, 10, 5, 5, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 6, 6, 10, 10, 20] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 118 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248326 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248326/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248326 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 91) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@@]34CN(C(=O)OC(C)(C)C)C[C@@H](C[C@H]3C2)O4)ccc1O) `ZINC001184248326.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184248326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248326/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184248326 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@@]34CN(C(=O)OC(C)(C)C)C[C@@H](C[C@H]3C2)O4)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 7, 5, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 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, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [19, 11, 11, 11, 6, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 22, 24, 24, 24, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 19, 19, 19, 11, 6, 6, 4, 4, 4, 4, 4, 4, 24, 24, 24, 24, 24, 24, 24, 24, 24, 4, 4, 4, 4, 4, 4, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 118 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248326 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184248326 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248326/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248326/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248326 Building ZINC001184248457 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248457' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248457 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184248457 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248457/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248457 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 92) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/92 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/92' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCc3ccc(=O)n(Cc4csc(C)n4)c3CC2)ccc1O) `ZINC001184248457.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184248457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248457/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184248457 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCc3ccc(=O)n(Cc4csc(C)n4)c3CC2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 11, 8, 5, 1, 1, 14, 1, 5, 8, 1, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [15, 12, 12, 12, 6, 1, 1, 1, 2, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12, 19, 19, 19, 19, 19, 8, 8, 8, 12, 12, 12, 12, 15, 15, 15, 12, 6, 6, 8, 8, 8, 8, 8, 8, 12, 12, 19, 19, 19, 19, 8, 8, 8, 8, 12, 12, 24] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 110 number of broken/clashed sets: 84 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248457 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248457/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248457 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 93) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/93 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/93' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCc3ccc(=O)n(Cc4csc(C)n4)c3CC2)ccc1O) `ZINC001184248457.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184248457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248457/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184248457 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCc3ccc(=O)n(Cc4csc(C)n4)c3CC2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 11, 8, 5, 1, 1, 14, 1, 5, 8, 1, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [12, 9, 9, 9, 5, 1, 1, 1, 2, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 14, 24, 24, 24, 24, 24, 10, 10, 10, 9, 9, 9, 9, 12, 12, 12, 9, 5, 5, 10, 10, 10, 10, 10, 10, 14, 14, 24, 24, 24, 24, 10, 10, 10, 10, 9, 9, 18] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 107 number of broken/clashed sets: 72 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248457 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184248457 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248457/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248457/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248457 Building ZINC001184248457 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248457' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248457 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184248457 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248457/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248457 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 92) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCc3ccc(=O)n(Cc4csc(C)n4)c3CC2)ccc1O) `ZINC001184248457.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184248457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248457/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184248457 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCc3ccc(=O)n(Cc4csc(C)n4)c3CC2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 11, 8, 5, 1, 1, 14, 1, 5, 8, 1, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [15, 12, 12, 12, 6, 1, 1, 1, 2, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12, 19, 19, 19, 19, 19, 8, 8, 8, 12, 12, 12, 12, 15, 15, 15, 12, 6, 6, 8, 8, 8, 8, 8, 8, 12, 12, 19, 19, 19, 19, 8, 8, 8, 8, 12, 12, 24] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 110 number of broken/clashed sets: 84 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248457 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248457/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248457 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 93) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCc3ccc(=O)n(Cc4csc(C)n4)c3CC2)ccc1O) `ZINC001184248457.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184248457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248457/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184248457 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCc3ccc(=O)n(Cc4csc(C)n4)c3CC2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 11, 8, 5, 1, 1, 14, 1, 5, 8, 1, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [12, 9, 9, 9, 5, 1, 1, 1, 2, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 14, 24, 24, 24, 24, 24, 10, 10, 10, 9, 9, 9, 9, 12, 12, 12, 9, 5, 5, 10, 10, 10, 10, 10, 10, 14, 14, 24, 24, 24, 24, 10, 10, 10, 10, 9, 9, 18] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 107 number of broken/clashed sets: 72 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248457 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184248457 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248457/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248457/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248457 Building ZINC001184248574 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248574' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248574 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184248574 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248574/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248574 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 94) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/94 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/94' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)N2Cc3ccnn3C[C@@H](COCc3csc(C)n3)C2)ccc1O) `ZINC001184248574.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184248574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184248574 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2Cc3ccnn3C[C@@H](COCc3csc(C)n3)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.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 8, 5, 5, 7, 5, 12, 5, 1, 1, 14, 1, 5, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [10, 6, 6, 6, 3, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 12, 22, 25, 25, 25, 25, 25, 4, 6, 6, 6, 6, 10, 10, 10, 6, 3, 3, 4, 4, 4, 4, 4, 4, 6, 6, 22, 22, 25, 25, 25, 25, 4, 4, 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, 55, 56, 57, 58]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248574 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248574/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248574 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 95) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/95 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/95' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2Cc3ccnn3C[C@@H](COCc3csc(C)n3)C2)ccc1O) `ZINC001184248574.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184248574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248574/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184248574 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2Cc3ccnn3C[C@@H](COCc3csc(C)n3)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.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 8, 5, 5, 7, 5, 12, 5, 1, 1, 14, 1, 5, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [12, 8, 8, 8, 4, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 13, 22, 29, 29, 29, 29, 29, 6, 8, 8, 8, 8, 12, 12, 12, 8, 4, 4, 6, 6, 6, 6, 6, 6, 11, 11, 22, 22, 29, 29, 29, 29, 6, 6, 8, 8, 16] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 132 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248574 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184248574 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248574/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248574/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248574 Building ZINC001184248574 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248574' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248574 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184248574 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248574/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248574 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 94) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/94: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)N2Cc3ccnn3C[C@@H](COCc3csc(C)n3)C2)ccc1O) `ZINC001184248574.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184248574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184248574 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2Cc3ccnn3C[C@@H](COCc3csc(C)n3)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.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 8, 5, 5, 7, 5, 12, 5, 1, 1, 14, 1, 5, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [10, 6, 6, 6, 3, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 12, 22, 25, 25, 25, 25, 25, 4, 6, 6, 6, 6, 10, 10, 10, 6, 3, 3, 4, 4, 4, 4, 4, 4, 6, 6, 22, 22, 25, 25, 25, 25, 4, 4, 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, 55, 56, 57, 58]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248574 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248574/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248574 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 95) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/95: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2Cc3ccnn3C[C@@H](COCc3csc(C)n3)C2)ccc1O) `ZINC001184248574.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184248574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248574/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184248574 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2Cc3ccnn3C[C@@H](COCc3csc(C)n3)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.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 8, 5, 5, 7, 5, 12, 5, 1, 1, 14, 1, 5, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [12, 8, 8, 8, 4, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 13, 22, 29, 29, 29, 29, 29, 6, 8, 8, 8, 8, 12, 12, 12, 8, 4, 4, 6, 6, 6, 6, 6, 6, 11, 11, 22, 22, 29, 29, 29, 29, 6, 6, 8, 8, 16] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 132 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248574 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184248574 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248574/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248574/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248574 Building ZINC001184248576 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248576' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248576 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184248576 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248576/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248576 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 96) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/96 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/96' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)N2Cc3ccnn3C[C@H](COCc3csc(C)n3)C2)ccc1O) `ZINC001184248576.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184248576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184248576 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2Cc3ccnn3C[C@H](COCc3csc(C)n3)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.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 8, 5, 5, 7, 5, 12, 5, 1, 1, 14, 1, 5, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [13, 7, 7, 7, 4, 1, 1, 1, 1, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 11, 21, 28, 28, 28, 28, 28, 6, 7, 7, 7, 7, 13, 13, 13, 7, 4, 4, 6, 6, 6, 6, 6, 6, 8, 8, 21, 21, 28, 28, 28, 28, 6, 6, 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, 55, 56, 57, 58]) total number of confs: 129 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248576 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248576/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248576 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 97) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/97 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/97' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2Cc3ccnn3C[C@H](COCc3csc(C)n3)C2)ccc1O) `ZINC001184248576.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184248576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248576/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184248576 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2Cc3ccnn3C[C@H](COCc3csc(C)n3)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.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 8, 5, 5, 7, 5, 12, 5, 1, 1, 14, 1, 5, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [14, 12, 12, 12, 6, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 10, 16, 19, 19, 19, 19, 19, 5, 12, 12, 12, 12, 14, 14, 14, 12, 6, 6, 5, 5, 5, 5, 5, 5, 7, 7, 16, 16, 19, 19, 19, 19, 5, 5, 12, 12, 24] 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248576 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184248576 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248576/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248576/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248576 Building ZINC001184248576 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248576' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248576 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184248576 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248576/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248576 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 96) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N2Cc3ccnn3C[C@H](COCc3csc(C)n3)C2)ccc1O) `ZINC001184248576.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184248576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184248576 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2Cc3ccnn3C[C@H](COCc3csc(C)n3)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.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 8, 5, 5, 7, 5, 12, 5, 1, 1, 14, 1, 5, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [13, 7, 7, 7, 4, 1, 1, 1, 1, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 11, 21, 28, 28, 28, 28, 28, 6, 7, 7, 7, 7, 13, 13, 13, 7, 4, 4, 6, 6, 6, 6, 6, 6, 8, 8, 21, 21, 28, 28, 28, 28, 6, 6, 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, 55, 56, 57, 58]) total number of confs: 129 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248576 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248576/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248576 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 97) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2Cc3ccnn3C[C@H](COCc3csc(C)n3)C2)ccc1O) `ZINC001184248576.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184248576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248576/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184248576 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2Cc3ccnn3C[C@H](COCc3csc(C)n3)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.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 8, 5, 5, 7, 5, 12, 5, 1, 1, 14, 1, 5, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [14, 12, 12, 12, 6, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 10, 16, 19, 19, 19, 19, 19, 5, 12, 12, 12, 12, 14, 14, 14, 12, 6, 6, 5, 5, 5, 5, 5, 5, 7, 7, 16, 16, 19, 19, 19, 19, 5, 5, 12, 12, 24] 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248576 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184248576 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248576/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248576/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248576 Building ZINC001184248600 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248600' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248600 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184248600 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248600/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248600 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 98) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/98 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/98' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2ncnc3c2c(I)nn3C(C)C)ccc1O) `ZINC001184248600.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184248600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184248600 none COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2ncnc3c2c(I)nn3C(C)C)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'I', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 8, 1, 8, 1, 1, 1, 18, 8, 8, 5, 5, 5, 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, 3, 7, 3, 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: [17, 6, 6, 6, 3, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 6, 6, 6, 6, 17, 17, 17, 6, 3, 3, 3, 6, 24, 24, 24, 24, 24, 24, 24, 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248600 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248600/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248600 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 99) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/99 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/99' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2ncnc3c2c(I)nn3C(C)C)ccc1O) `ZINC001184248600.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184248600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248600/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184248600 none COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2ncnc3c2c(I)nn3C(C)C)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'I', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 8, 1, 8, 1, 1, 1, 18, 8, 8, 5, 5, 5, 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, 3, 7, 3, 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: [17, 6, 6, 6, 3, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 6, 6, 6, 6, 17, 17, 17, 6, 3, 3, 3, 6, 24, 24, 24, 24, 24, 24, 24, 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248600 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184248600 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248600/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248600/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248600 Building ZINC001184248600 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248600' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248600 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184248600 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248600/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248600 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 98) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/98: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2ncnc3c2c(I)nn3C(C)C)ccc1O) `ZINC001184248600.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184248600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184248600 none COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2ncnc3c2c(I)nn3C(C)C)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'I', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 8, 1, 8, 1, 1, 1, 18, 8, 8, 5, 5, 5, 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, 3, 7, 3, 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: [17, 6, 6, 6, 3, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 6, 6, 6, 6, 17, 17, 17, 6, 3, 3, 3, 6, 24, 24, 24, 24, 24, 24, 24, 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248600 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248600/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248600 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 99) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/99: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2ncnc3c2c(I)nn3C(C)C)ccc1O) `ZINC001184248600.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184248600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248600/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184248600 none COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2ncnc3c2c(I)nn3C(C)C)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'I', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 8, 1, 8, 1, 1, 1, 18, 8, 8, 5, 5, 5, 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, 3, 7, 3, 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: [17, 6, 6, 6, 3, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 6, 6, 6, 6, 17, 17, 17, 6, 3, 3, 3, 6, 24, 24, 24, 24, 24, 24, 24, 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248600 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184248600 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248600/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248600/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248600 Building ZINC001184248612 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248612' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248612 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184248612 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248612/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248612 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 100) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/100 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/100' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@]3(C2)C[C@@H](NC(=O)c2ccsc2)CCO3)ccc1O) `ZINC001184248612.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184248612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184248612 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@]3(C2)C[C@@H](NC(=O)c2ccsc2)CCO3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 14, 1, 5, 5, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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, 9, 9, 9, 5, 1, 1, 1, 1, 4, 5, 10, 10, 10, 10, 10, 10, 10, 10, 13, 13, 13, 25, 25, 25, 25, 10, 10, 10, 9, 9, 9, 9, 11, 11, 11, 9, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 13, 25, 25, 25, 10, 10, 10, 10, 9, 9, 18] 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]) total number of confs: 93 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248612 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248612/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248612 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 101) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/101 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/101' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@]3(C2)C[C@@H](NC(=O)c2ccsc2)CCO3)ccc1O) `ZINC001184248612.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184248612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248612/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184248612 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@]3(C2)C[C@@H](NC(=O)c2ccsc2)CCO3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 14, 1, 5, 5, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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: [12, 8, 8, 8, 4, 1, 1, 1, 1, 3, 4, 9, 9, 9, 9, 9, 9, 9, 9, 15, 15, 15, 29, 29, 29, 29, 9, 9, 9, 8, 8, 8, 8, 12, 12, 12, 8, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 15, 29, 29, 29, 9, 9, 9, 9, 8, 8, 16] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 103 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248612 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184248612 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248612/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248612/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248612 Building ZINC001184248612 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248612' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248612 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184248612 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248612/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248612 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 100) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@]3(C2)C[C@@H](NC(=O)c2ccsc2)CCO3)ccc1O) `ZINC001184248612.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184248612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184248612 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@]3(C2)C[C@@H](NC(=O)c2ccsc2)CCO3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 14, 1, 5, 5, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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, 9, 9, 9, 5, 1, 1, 1, 1, 4, 5, 10, 10, 10, 10, 10, 10, 10, 10, 13, 13, 13, 25, 25, 25, 25, 10, 10, 10, 9, 9, 9, 9, 11, 11, 11, 9, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 13, 25, 25, 25, 10, 10, 10, 10, 9, 9, 18] 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]) total number of confs: 93 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248612 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248612/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248612 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 101) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@]3(C2)C[C@@H](NC(=O)c2ccsc2)CCO3)ccc1O) `ZINC001184248612.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184248612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248612/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184248612 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@]3(C2)C[C@@H](NC(=O)c2ccsc2)CCO3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 14, 1, 5, 5, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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: [12, 8, 8, 8, 4, 1, 1, 1, 1, 3, 4, 9, 9, 9, 9, 9, 9, 9, 9, 15, 15, 15, 29, 29, 29, 29, 9, 9, 9, 8, 8, 8, 8, 12, 12, 12, 8, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 15, 29, 29, 29, 9, 9, 9, 9, 8, 8, 16] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 103 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248612 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184248612 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248612/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248612/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248612 Building ZINC001184248646 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248646' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248646 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184248646 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248646/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248646 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 102) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/102 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/102' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC[C@H]1c2c(cnn2CC2CCOCC2)CCN1C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1) `ZINC001184248646.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184248646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184248646 none CCOC[C@H]1c2c(cnn2CC2CCOCC2)CCN1C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 1, 1, 1, 8, 8, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 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, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 14, 14, 14, 14, 14, 3, 3, 3, 1, 3, 1, 1, 1, 4, 7, 7, 7, 7, 7, 7, 10, 7, 8, 8, 8, 8, 8, 5, 5, 3, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 3, 3, 3, 3, 4, 4, 7, 7, 14, 10, 10, 10, 7] 100 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 103 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248646 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248646/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248646 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 103) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/103 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/103' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC[C@H]1c2c(cnn2CC2CCOCC2)CCN1C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1) `ZINC001184248646.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184248646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248646/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184248646 none CCOC[C@H]1c2c(cnn2CC2CCOCC2)CCN1C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 1, 1, 1, 8, 8, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 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, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 11, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 19, 19, 19, 19, 19, 3, 3, 3, 1, 3, 1, 1, 1, 5, 10, 10, 10, 10, 10, 10, 15, 10, 12, 12, 12, 12, 12, 7, 7, 3, 11, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 5, 5, 10, 10, 20, 15, 15, 15, 10] 100 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 150 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248646 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184248646 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248646/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248646/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248646 Building ZINC001184248646 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248646' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248646 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184248646 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248646/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248646 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 102) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCOC[C@H]1c2c(cnn2CC2CCOCC2)CCN1C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1) `ZINC001184248646.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184248646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184248646 none CCOC[C@H]1c2c(cnn2CC2CCOCC2)CCN1C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 1, 1, 1, 8, 8, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 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, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 14, 14, 14, 14, 14, 3, 3, 3, 1, 3, 1, 1, 1, 4, 7, 7, 7, 7, 7, 7, 10, 7, 8, 8, 8, 8, 8, 5, 5, 3, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 3, 3, 3, 3, 4, 4, 7, 7, 14, 10, 10, 10, 7] 100 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 103 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248646 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248646/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248646 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 103) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCOC[C@H]1c2c(cnn2CC2CCOCC2)CCN1C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1) `ZINC001184248646.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184248646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248646/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184248646 none CCOC[C@H]1c2c(cnn2CC2CCOCC2)CCN1C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 1, 1, 1, 8, 8, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 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, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 11, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 19, 19, 19, 19, 19, 3, 3, 3, 1, 3, 1, 1, 1, 5, 10, 10, 10, 10, 10, 10, 15, 10, 12, 12, 12, 12, 12, 7, 7, 3, 11, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 5, 5, 10, 10, 20, 15, 15, 15, 10] 100 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 150 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248646 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184248646 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248646/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248646/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248646 Building ZINC001184248647 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248647' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248647 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184248647 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248647/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248647 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 104) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/104 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/104' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC[C@@H]1c2c(cnn2CC2CCOCC2)CCN1C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1) `ZINC001184248647.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184248647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248647/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184248647 none CCOC[C@@H]1c2c(cnn2CC2CCOCC2)CCN1C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 1, 1, 1, 8, 8, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 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, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 19, 19, 19, 19, 19, 3, 3, 3, 1, 3, 1, 1, 1, 5, 10, 10, 10, 10, 10, 10, 16, 10, 10, 10, 10, 10, 10, 6, 6, 3, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 5, 5, 10, 10, 20, 16, 16, 16, 10] 100 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 145 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248647 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248647/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248647 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 105) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/105 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/105' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC[C@@H]1c2c(cnn2CC2CCOCC2)CCN1C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1) `ZINC001184248647.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184248647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248647/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184248647 none CCOC[C@@H]1c2c(cnn2CC2CCOCC2)CCN1C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 1, 1, 1, 8, 8, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 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, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 13, 13, 13, 13, 13, 3, 3, 3, 1, 3, 1, 1, 1, 4, 7, 7, 7, 7, 7, 7, 10, 7, 6, 6, 6, 6, 6, 4, 4, 3, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 3, 3, 3, 4, 4, 7, 7, 14, 10, 10, 10, 7] 100 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 97 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248647 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184248647 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248647/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248647/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248647 Building ZINC001184248647 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248647' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248647 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184248647 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248647/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248647 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 104) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCOC[C@@H]1c2c(cnn2CC2CCOCC2)CCN1C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1) `ZINC001184248647.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184248647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248647/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184248647 none CCOC[C@@H]1c2c(cnn2CC2CCOCC2)CCN1C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 1, 1, 1, 8, 8, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 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, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 19, 19, 19, 19, 19, 3, 3, 3, 1, 3, 1, 1, 1, 5, 10, 10, 10, 10, 10, 10, 16, 10, 10, 10, 10, 10, 10, 6, 6, 3, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 5, 5, 10, 10, 20, 16, 16, 16, 10] 100 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 145 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248647 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248647/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248647 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 105) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCOC[C@@H]1c2c(cnn2CC2CCOCC2)CCN1C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1) `ZINC001184248647.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184248647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248647/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184248647 none CCOC[C@@H]1c2c(cnn2CC2CCOCC2)CCN1C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 1, 1, 1, 8, 8, 5, 5, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 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, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 13, 13, 13, 13, 13, 3, 3, 3, 1, 3, 1, 1, 1, 4, 7, 7, 7, 7, 7, 7, 10, 7, 6, 6, 6, 6, 6, 4, 4, 3, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 3, 3, 3, 4, 4, 7, 7, 14, 10, 10, 10, 7] 100 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 97 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248647 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184248647 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248647/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248647/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248647 Building ZINC001184248800 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248800' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248800 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184248800 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248800/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248800 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 106) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/106 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/106' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2nc([S@@](C)=O)nc(Cl)c2Br)ccc1O) `ZINC001184248800.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184248800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184248800 none COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2nc([S@@](C)=O)nc(Cl)c2Br)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', 'N.ar', 'C.ar', 'S.o', 'C.3', 'O.2', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'Br', '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: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 8, 1, 14, 5, 11, 8, 1, 16, 1, 17, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 3, 3, 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: [15, 6, 6, 6, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 23, 23, 4, 4, 4, 4, 4, 6, 6, 6, 6, 15, 15, 15, 6, 3, 3, 2, 23, 23, 23, 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]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248800 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248800/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248800 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 107) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/107 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/107' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2nc([S@@](C)=O)nc(Cl)c2Br)ccc1O) `ZINC001184248800.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184248800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248800/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184248800 none COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2nc([S@@](C)=O)nc(Cl)c2Br)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', 'N.ar', 'C.ar', 'S.o', 'C.3', 'O.2', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'Br', '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: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 8, 1, 14, 5, 11, 8, 1, 16, 1, 17, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 3, 3, 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: [16, 6, 6, 6, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 26, 26, 4, 4, 4, 4, 4, 6, 6, 6, 6, 16, 16, 16, 6, 3, 3, 2, 26, 26, 26, 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248800 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184248800 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248800/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248800/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248800 Building ZINC001184248800 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248800' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248800 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184248800 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248800/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248800 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 106) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2nc([S@@](C)=O)nc(Cl)c2Br)ccc1O) `ZINC001184248800.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184248800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184248800 none COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2nc([S@@](C)=O)nc(Cl)c2Br)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', 'N.ar', 'C.ar', 'S.o', 'C.3', 'O.2', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'Br', '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: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 8, 1, 14, 5, 11, 8, 1, 16, 1, 17, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 3, 3, 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: [15, 6, 6, 6, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 23, 23, 4, 4, 4, 4, 4, 6, 6, 6, 6, 15, 15, 15, 6, 3, 3, 2, 23, 23, 23, 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]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248800 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248800/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248800 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 107) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2nc([S@@](C)=O)nc(Cl)c2Br)ccc1O) `ZINC001184248800.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184248800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248800/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184248800 none COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2nc([S@@](C)=O)nc(Cl)c2Br)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', 'N.ar', 'C.ar', 'S.o', 'C.3', 'O.2', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'Br', '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: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 8, 1, 14, 5, 11, 8, 1, 16, 1, 17, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 3, 3, 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: [16, 6, 6, 6, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 26, 26, 4, 4, 4, 4, 4, 6, 6, 6, 6, 16, 16, 16, 6, 3, 3, 2, 26, 26, 26, 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248800 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184248800 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248800/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248800/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248800 Building ZINC001184248801 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248801' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248801 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184248801 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248801/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248801 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 108) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/108 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/108' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2nc([S@](C)=O)nc(Cl)c2Br)ccc1O) `ZINC001184248801.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184248801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184248801 none COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2nc([S@](C)=O)nc(Cl)c2Br)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', 'N.ar', 'C.ar', 'S.o', 'C.3', 'O.2', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'Br', '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: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 8, 1, 14, 5, 11, 8, 1, 16, 1, 17, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 3, 3, 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: [16, 6, 6, 6, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 26, 26, 4, 4, 4, 4, 4, 6, 6, 6, 6, 16, 16, 16, 6, 3, 3, 2, 26, 26, 26, 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248801 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248801/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248801 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 109) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/109 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/109' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2nc([S@](C)=O)nc(Cl)c2Br)ccc1O) `ZINC001184248801.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184248801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248801/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184248801 none COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2nc([S@](C)=O)nc(Cl)c2Br)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', 'N.ar', 'C.ar', 'S.o', 'C.3', 'O.2', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'Br', '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: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 8, 1, 14, 5, 11, 8, 1, 16, 1, 17, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 3, 3, 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: [15, 6, 6, 6, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 23, 23, 4, 4, 4, 4, 4, 6, 6, 6, 6, 15, 15, 15, 6, 3, 3, 2, 23, 23, 23, 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]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248801 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184248801 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248801/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248801/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248801 Building ZINC001184248801 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248801' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248801 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184248801 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248801/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248801 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 108) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2nc([S@](C)=O)nc(Cl)c2Br)ccc1O) `ZINC001184248801.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184248801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184248801 none COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2nc([S@](C)=O)nc(Cl)c2Br)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', 'N.ar', 'C.ar', 'S.o', 'C.3', 'O.2', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'Br', '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: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 8, 1, 14, 5, 11, 8, 1, 16, 1, 17, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 3, 3, 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: [16, 6, 6, 6, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 26, 26, 4, 4, 4, 4, 4, 6, 6, 6, 6, 16, 16, 16, 6, 3, 3, 2, 26, 26, 26, 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248801 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248801/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248801 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 109) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2nc([S@](C)=O)nc(Cl)c2Br)ccc1O) `ZINC001184248801.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184248801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248801/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184248801 none COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2nc([S@](C)=O)nc(Cl)c2Br)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', 'N.ar', 'C.ar', 'S.o', 'C.3', 'O.2', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'Br', '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: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 8, 1, 14, 5, 11, 8, 1, 16, 1, 17, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 3, 3, 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: [15, 6, 6, 6, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 23, 23, 4, 4, 4, 4, 4, 6, 6, 6, 6, 15, 15, 15, 6, 3, 3, 2, 23, 23, 23, 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]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248801 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184248801 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248801/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248801/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248801 Building ZINC001184248840 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248840' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248840 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184248840 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248840/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248840 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 110) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/110 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/110' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nnc2c1CCN(C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)[C@H]2COCc1ccccc1) `ZINC001184248840.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184248840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184248840 none CCn1nnc2c1CCN(C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)[C@H]2COCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 9, 6, 2, 2, 2, 4, 7, 18, 25, 25, 18, 25, 25, 4, 4, 4, 4, 4, 2, 2, 2, 2, 3, 3, 6, 6, 12, 9, 9, 9, 6, 4, 4, 18, 18, 25, 25, 18, 25, 25] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248840 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248840/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248840 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 111) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/111 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/111' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nnc2c1CCN(C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)[C@H]2COCc1ccccc1) `ZINC001184248840.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184248840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248840/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184248840 none CCn1nnc2c1CCN(C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)[C@H]2COCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 9, 6, 2, 2, 2, 4, 9, 22, 28, 28, 22, 28, 28, 4, 4, 4, 4, 4, 2, 2, 2, 2, 3, 3, 6, 6, 12, 9, 9, 9, 6, 4, 4, 22, 22, 28, 28, 22, 28, 28] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248840 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184248840 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248840/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248840/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248840 Building ZINC001184248840 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248840' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248840 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184248840 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248840/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248840 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 110) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCn1nnc2c1CCN(C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)[C@H]2COCc1ccccc1) `ZINC001184248840.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184248840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184248840 none CCn1nnc2c1CCN(C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)[C@H]2COCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 9, 6, 2, 2, 2, 4, 7, 18, 25, 25, 18, 25, 25, 4, 4, 4, 4, 4, 2, 2, 2, 2, 3, 3, 6, 6, 12, 9, 9, 9, 6, 4, 4, 18, 18, 25, 25, 18, 25, 25] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248840 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248840/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248840 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 111) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCn1nnc2c1CCN(C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)[C@H]2COCc1ccccc1) `ZINC001184248840.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184248840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248840/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184248840 none CCn1nnc2c1CCN(C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)[C@H]2COCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 9, 6, 2, 2, 2, 4, 9, 22, 28, 28, 22, 28, 28, 4, 4, 4, 4, 4, 2, 2, 2, 2, 3, 3, 6, 6, 12, 9, 9, 9, 6, 4, 4, 22, 22, 28, 28, 22, 28, 28] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248840 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184248840 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248840/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248840/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248840 Building ZINC001184248841 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248841' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248841 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184248841 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248841/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248841 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 112) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/112 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/112' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nnc2c1CCN(C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)[C@@H]2COCc1ccccc1) `ZINC001184248841.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184248841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184248841 none CCn1nnc2c1CCN(C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)[C@@H]2COCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 10, 6, 2, 2, 2, 4, 9, 19, 23, 23, 19, 23, 23, 4, 4, 4, 4, 4, 2, 2, 2, 2, 3, 3, 6, 6, 12, 10, 10, 10, 6, 4, 4, 19, 19, 23, 23, 19, 23, 23] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248841 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248841/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248841 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 113) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/113 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/113' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nnc2c1CCN(C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)[C@@H]2COCc1ccccc1) `ZINC001184248841.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184248841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248841/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184248841 none CCn1nnc2c1CCN(C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)[C@@H]2COCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 12, 6, 2, 2, 2, 4, 8, 17, 21, 21, 17, 21, 21, 4, 4, 4, 4, 4, 2, 2, 2, 2, 3, 3, 6, 6, 12, 12, 12, 12, 6, 4, 4, 17, 17, 21, 21, 17, 21, 21] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248841 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184248841 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248841/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248841/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248841 Building ZINC001184248841 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248841' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248841 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184248841 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248841/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248841 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 112) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCn1nnc2c1CCN(C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)[C@@H]2COCc1ccccc1) `ZINC001184248841.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184248841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184248841 none CCn1nnc2c1CCN(C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)[C@@H]2COCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 10, 6, 2, 2, 2, 4, 9, 19, 23, 23, 19, 23, 23, 4, 4, 4, 4, 4, 2, 2, 2, 2, 3, 3, 6, 6, 12, 10, 10, 10, 6, 4, 4, 19, 19, 23, 23, 19, 23, 23] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248841 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248841/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248841 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 113) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCn1nnc2c1CCN(C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)[C@@H]2COCc1ccccc1) `ZINC001184248841.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184248841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248841/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184248841 none CCn1nnc2c1CCN(C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)[C@@H]2COCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 12, 6, 2, 2, 2, 4, 8, 17, 21, 21, 17, 21, 21, 4, 4, 4, 4, 4, 2, 2, 2, 2, 3, 3, 6, 6, 12, 12, 12, 12, 6, 4, 4, 17, 17, 21, 21, 17, 21, 21] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248841 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184248841 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248841/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248841/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184248841 Building ZINC001184249105 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249105' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249105 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184249105 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249105/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249105 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 114) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/114 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/114' -> `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]2CCC23CCNCC3)S(=O)(=O)c2ccccc2)ccc1O) `ZINC001184249105.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184249105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184249105 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N([C@@H]2CCC23CCNCC3)S(=O)(=O)c2ccccc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 10, 5, 5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 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, 6] 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 6, 6, 3, 1, 1, 1, 1, 1, 1, 3, 6, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 6, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 6, 6, 12] 36 rigid atoms, others: [5, 6, 7, 8, 9, 10, 55, 54, 56, 57, 21, 22, 23, 24, 25, 26, 27, 28, 29, 53] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 58, 59, 60]) total number of confs: 49 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249105 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249105/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249105 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 115) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/115 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/115' -> `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]2CCC23CCNCC3)S(=O)(=O)c2ccccc2)ccc1O) `ZINC001184249105.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184249105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249105/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184249105 none COc1cc(C[C@]([O-])([SiH3])C(=O)N([C@@H]2CCC23CCNCC3)S(=O)(=O)c2ccccc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 10, 5, 5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 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, 6] 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 6, 6, 3, 1, 1, 1, 1, 1, 1, 4, 7, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 15, 15, 15, 6, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 2, 6, 6, 12] 62 rigid atoms, others: [5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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: 62 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249105 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184249105 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249105/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249105/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249105 Building ZINC001184249105 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249105' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249105 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184249105 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249105/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249105 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 114) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)N([C@@H]2CCC23CCNCC3)S(=O)(=O)c2ccccc2)ccc1O) `ZINC001184249105.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184249105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184249105 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N([C@@H]2CCC23CCNCC3)S(=O)(=O)c2ccccc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 10, 5, 5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 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, 6] 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 6, 6, 3, 1, 1, 1, 1, 1, 1, 3, 6, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 6, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 6, 6, 12] 36 rigid atoms, others: [5, 6, 7, 8, 9, 10, 55, 54, 56, 57, 21, 22, 23, 24, 25, 26, 27, 28, 29, 53] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 58, 59, 60]) total number of confs: 49 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249105 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249105/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249105 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 115) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N([C@@H]2CCC23CCNCC3)S(=O)(=O)c2ccccc2)ccc1O) `ZINC001184249105.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184249105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249105/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184249105 none COc1cc(C[C@]([O-])([SiH3])C(=O)N([C@@H]2CCC23CCNCC3)S(=O)(=O)c2ccccc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 10, 5, 5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 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, 6] 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 6, 6, 3, 1, 1, 1, 1, 1, 1, 4, 7, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 15, 15, 15, 6, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 2, 6, 6, 12] 62 rigid atoms, others: [5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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: 62 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249105 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184249105 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249105/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249105/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249105 Building ZINC001184249106 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249106' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249106 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184249106 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249106/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249106 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 116) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/116 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/116' -> `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]2CCC23CCNCC3)S(=O)(=O)c2ccccc2)ccc1O) `ZINC001184249106.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184249106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184249106 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N([C@H]2CCC23CCNCC3)S(=O)(=O)c2ccccc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 10, 5, 5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 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, 6] 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 6, 6, 3, 1, 1, 1, 1, 1, 1, 3, 8, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 16, 16, 16, 6, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 2, 2, 6, 6, 12] 62 rigid atoms, others: [5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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: 64 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249106 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249106/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249106 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 117) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/117 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/117' -> `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]2CCC23CCNCC3)S(=O)(=O)c2ccccc2)ccc1O) `ZINC001184249106.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184249106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249106/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184249106 none COc1cc(C[C@]([O-])([SiH3])C(=O)N([C@H]2CCC23CCNCC3)S(=O)(=O)c2ccccc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 10, 5, 5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 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, 6] 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 6, 6, 3, 1, 1, 1, 1, 1, 1, 2, 6, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 6, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 6, 6, 12] 36 rigid atoms, others: [5, 6, 7, 8, 9, 10, 55, 54, 56, 57, 21, 22, 23, 24, 25, 26, 27, 28, 29, 53] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 58, 59, 60]) total number of confs: 48 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249106 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184249106 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249106/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249106/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249106 Building ZINC001184249106 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249106' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249106 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184249106 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249106/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249106 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 116) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)N([C@H]2CCC23CCNCC3)S(=O)(=O)c2ccccc2)ccc1O) `ZINC001184249106.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184249106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184249106 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N([C@H]2CCC23CCNCC3)S(=O)(=O)c2ccccc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 10, 5, 5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 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, 6] 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 6, 6, 3, 1, 1, 1, 1, 1, 1, 3, 8, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 16, 16, 16, 6, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 2, 2, 6, 6, 12] 62 rigid atoms, others: [5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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: 64 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249106 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249106/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249106 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 117) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N([C@H]2CCC23CCNCC3)S(=O)(=O)c2ccccc2)ccc1O) `ZINC001184249106.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184249106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249106/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184249106 none COc1cc(C[C@]([O-])([SiH3])C(=O)N([C@H]2CCC23CCNCC3)S(=O)(=O)c2ccccc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 10, 5, 5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 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, 6] 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 6, 6, 3, 1, 1, 1, 1, 1, 1, 2, 6, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 6, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 6, 6, 12] 36 rigid atoms, others: [5, 6, 7, 8, 9, 10, 55, 54, 56, 57, 21, 22, 23, 24, 25, 26, 27, 28, 29, 53] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 58, 59, 60]) total number of confs: 48 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249106 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184249106 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249106/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249106/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249106 Building ZINC001184249372 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249372' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249372 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184249372 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249372/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249372 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 118) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/118 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/118' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC3(CC2)OCC(=O)N(Cc2cccc(C)n2)[C@@H]3C)ccc1O) `ZINC001184249372.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184249372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001184249372 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC3(CC2)OCC(=O)N(Cc2cccc(C)n2)[C@@H]3C)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 8, 5, 7, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 8, 8, 8, 4, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 17, 17, 17, 17, 17, 17, 4, 4, 4, 8, 8, 8, 8, 13, 13, 13, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 17, 17, 17, 17, 17, 17, 4, 4, 4, 8, 8, 16] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 91 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249372 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249372/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249372 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 119) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/119 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/119' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC3(CC2)OCC(=O)N(Cc2cccc(C)n2)[C@@H]3C)ccc1O) `ZINC001184249372.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184249372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249372/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001184249372 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC3(CC2)OCC(=O)N(Cc2cccc(C)n2)[C@@H]3C)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 8, 5, 7, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 9, 5, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 20, 20, 20, 20, 20, 20, 5, 5, 5, 9, 9, 9, 9, 15, 15, 15, 9, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 20, 20, 20, 20, 20, 20, 5, 5, 5, 9, 9, 18] 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, 60, 61, 62, 63, 64, 65]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249372 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184249372 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249372/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249372/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249372 Building ZINC001184249372 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249372' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249372 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184249372 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249372/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249372 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 118) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC3(CC2)OCC(=O)N(Cc2cccc(C)n2)[C@@H]3C)ccc1O) `ZINC001184249372.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184249372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001184249372 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC3(CC2)OCC(=O)N(Cc2cccc(C)n2)[C@@H]3C)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 8, 5, 7, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 8, 8, 8, 4, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 17, 17, 17, 17, 17, 17, 4, 4, 4, 8, 8, 8, 8, 13, 13, 13, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 17, 17, 17, 17, 17, 17, 4, 4, 4, 8, 8, 16] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 91 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249372 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249372/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249372 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 119) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC3(CC2)OCC(=O)N(Cc2cccc(C)n2)[C@@H]3C)ccc1O) `ZINC001184249372.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184249372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249372/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001184249372 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC3(CC2)OCC(=O)N(Cc2cccc(C)n2)[C@@H]3C)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 8, 5, 7, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 9, 5, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 20, 20, 20, 20, 20, 20, 5, 5, 5, 9, 9, 9, 9, 15, 15, 15, 9, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 20, 20, 20, 20, 20, 20, 5, 5, 5, 9, 9, 18] 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, 60, 61, 62, 63, 64, 65]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249372 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184249372 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249372/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249372/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249372 Building ZINC001184249385 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249385' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249385 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184249385 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249385/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249385 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 120) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/120 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/120' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC3(CC2)OCC(=O)N(Cc2cccc(C)n2)[C@H]3C)ccc1O) `ZINC001184249385.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184249385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001184249385 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC3(CC2)OCC(=O)N(Cc2cccc(C)n2)[C@H]3C)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 8, 5, 7, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 11, 11, 11, 6, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 19, 19, 19, 19, 19, 19, 4, 4, 4, 11, 11, 11, 11, 17, 17, 17, 11, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 19, 19, 19, 19, 19, 19, 4, 4, 4, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 116 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249385 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249385/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249385 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 121) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/121 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/121' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC3(CC2)OCC(=O)N(Cc2cccc(C)n2)[C@H]3C)ccc1O) `ZINC001184249385.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184249385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249385/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001184249385 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC3(CC2)OCC(=O)N(Cc2cccc(C)n2)[C@H]3C)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 8, 5, 7, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [14, 10, 10, 10, 5, 1, 1, 1, 1, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 18, 18, 18, 18, 18, 18, 6, 6, 6, 10, 10, 10, 10, 14, 14, 14, 10, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 18, 18, 18, 18, 18, 18, 6, 6, 6, 10, 10, 20] 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, 60, 61, 62, 63, 64, 65]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249385 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184249385 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249385/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249385/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249385 Building ZINC001184249385 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249385' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249385 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184249385 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249385/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249385 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 120) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC3(CC2)OCC(=O)N(Cc2cccc(C)n2)[C@H]3C)ccc1O) `ZINC001184249385.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184249385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001184249385 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC3(CC2)OCC(=O)N(Cc2cccc(C)n2)[C@H]3C)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 8, 5, 7, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 11, 11, 11, 6, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 19, 19, 19, 19, 19, 19, 4, 4, 4, 11, 11, 11, 11, 17, 17, 17, 11, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 19, 19, 19, 19, 19, 19, 4, 4, 4, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 116 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249385 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249385/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249385 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 121) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC3(CC2)OCC(=O)N(Cc2cccc(C)n2)[C@H]3C)ccc1O) `ZINC001184249385.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184249385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249385/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001184249385 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC3(CC2)OCC(=O)N(Cc2cccc(C)n2)[C@H]3C)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 8, 5, 7, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [14, 10, 10, 10, 5, 1, 1, 1, 1, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 18, 18, 18, 18, 18, 18, 6, 6, 6, 10, 10, 10, 10, 14, 14, 14, 10, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 18, 18, 18, 18, 18, 18, 6, 6, 6, 10, 10, 20] 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, 60, 61, 62, 63, 64, 65]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249385 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184249385 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249385/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249385/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249385 Building ZINC001184249391 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184249391 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 122) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/122 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/122' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O) `ZINC001184249391.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184249391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184249391 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [15, 8, 8, 8, 5, 1, 1, 1, 1, 2, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 19, 19, 19, 19, 19, 19, 6, 8, 8, 8, 8, 15, 15, 15, 8, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 19, 19, 19, 19, 19, 19, 6, 6, 8, 8, 16] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 101 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 123) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/123 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/123' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O) `ZINC001184249391.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184249391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184249391 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [15, 8, 8, 8, 5, 1, 1, 1, 1, 2, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 19, 19, 19, 19, 19, 19, 6, 8, 8, 8, 8, 15, 15, 15, 8, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 19, 19, 19, 19, 19, 19, 6, 6, 8, 8, 16] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 101 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 124) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/124 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/124' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O) `ZINC001184249391.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184249391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184249391 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 10, 10, 10, 5, 1, 1, 1, 1, 3, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 11, 20, 20, 20, 20, 20, 20, 8, 10, 10, 10, 10, 13, 13, 13, 10, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 11, 11, 20, 20, 20, 20, 20, 20, 8, 8, 10, 10, 20] 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, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 100 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 125) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/125 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/125' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O) `ZINC001184249391.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184249391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184249391 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 10, 10, 10, 5, 1, 1, 1, 1, 3, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 11, 20, 20, 20, 20, 20, 20, 8, 10, 10, 10, 10, 13, 13, 13, 10, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 11, 11, 20, 20, 20, 20, 20, 20, 8, 8, 10, 10, 20] 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, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 100 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184249391 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391 Building ZINC001184249391 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184249391 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 122) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O) `ZINC001184249391.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184249391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184249391 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [15, 8, 8, 8, 5, 1, 1, 1, 1, 2, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 19, 19, 19, 19, 19, 19, 6, 8, 8, 8, 8, 15, 15, 15, 8, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 19, 19, 19, 19, 19, 19, 6, 6, 8, 8, 16] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 101 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 123) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O) `ZINC001184249391.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184249391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184249391 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [15, 8, 8, 8, 5, 1, 1, 1, 1, 2, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 19, 19, 19, 19, 19, 19, 6, 8, 8, 8, 8, 15, 15, 15, 8, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 19, 19, 19, 19, 19, 19, 6, 6, 8, 8, 16] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 101 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 124) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/124: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O) `ZINC001184249391.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184249391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184249391 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 10, 10, 10, 5, 1, 1, 1, 1, 3, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 11, 20, 20, 20, 20, 20, 20, 8, 10, 10, 10, 10, 13, 13, 13, 10, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 11, 11, 20, 20, 20, 20, 20, 20, 8, 8, 10, 10, 20] 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, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 100 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 125) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/125: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O) `ZINC001184249391.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184249391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184249391 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 10, 10, 10, 5, 1, 1, 1, 1, 3, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 11, 20, 20, 20, 20, 20, 20, 8, 10, 10, 10, 10, 13, 13, 13, 10, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 11, 11, 20, 20, 20, 20, 20, 20, 8, 8, 10, 10, 20] 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, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 100 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184249391 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391 Building ZINC001184249391 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184249391 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 122) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O) `ZINC001184249391.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184249391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184249391 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [15, 8, 8, 8, 5, 1, 1, 1, 1, 2, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 19, 19, 19, 19, 19, 19, 6, 8, 8, 8, 8, 15, 15, 15, 8, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 19, 19, 19, 19, 19, 19, 6, 6, 8, 8, 16] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 101 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 123) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O) `ZINC001184249391.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184249391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184249391 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [15, 8, 8, 8, 5, 1, 1, 1, 1, 2, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 19, 19, 19, 19, 19, 19, 6, 8, 8, 8, 8, 15, 15, 15, 8, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 19, 19, 19, 19, 19, 19, 6, 6, 8, 8, 16] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 101 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 124) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/124: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O) `ZINC001184249391.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184249391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184249391 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 10, 10, 10, 5, 1, 1, 1, 1, 3, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 11, 20, 20, 20, 20, 20, 20, 8, 10, 10, 10, 10, 13, 13, 13, 10, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 11, 11, 20, 20, 20, 20, 20, 20, 8, 8, 10, 10, 20] 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, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 100 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 125) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/125: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O) `ZINC001184249391.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184249391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184249391 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 10, 10, 10, 5, 1, 1, 1, 1, 3, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 11, 20, 20, 20, 20, 20, 20, 8, 10, 10, 10, 10, 13, 13, 13, 10, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 11, 11, 20, 20, 20, 20, 20, 20, 8, 8, 10, 10, 20] 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, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 100 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184249391 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391 Building ZINC001184249391 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184249391 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 122) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O) `ZINC001184249391.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184249391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184249391 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [15, 8, 8, 8, 5, 1, 1, 1, 1, 2, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 19, 19, 19, 19, 19, 19, 6, 8, 8, 8, 8, 15, 15, 15, 8, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 19, 19, 19, 19, 19, 19, 6, 6, 8, 8, 16] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 101 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 123) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O) `ZINC001184249391.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184249391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184249391 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [15, 8, 8, 8, 5, 1, 1, 1, 1, 2, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 19, 19, 19, 19, 19, 19, 6, 8, 8, 8, 8, 15, 15, 15, 8, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 19, 19, 19, 19, 19, 19, 6, 6, 8, 8, 16] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 101 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 124) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/124: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O) `ZINC001184249391.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184249391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184249391 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 10, 10, 10, 5, 1, 1, 1, 1, 3, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 11, 20, 20, 20, 20, 20, 20, 8, 10, 10, 10, 10, 13, 13, 13, 10, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 11, 11, 20, 20, 20, 20, 20, 20, 8, 8, 10, 10, 20] 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, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 100 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 125) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/125: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O) `ZINC001184249391.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184249391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184249391 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 10, 10, 10, 5, 1, 1, 1, 1, 3, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 11, 20, 20, 20, 20, 20, 20, 8, 10, 10, 10, 10, 13, 13, 13, 10, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 11, 11, 20, 20, 20, 20, 20, 20, 8, 8, 10, 10, 20] 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, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 100 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184249391 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249391 Building ZINC001184249436 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184249436 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 126) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/126 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/126' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O) `ZINC001184249436.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184249436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184249436 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 8, 8, 4, 1, 1, 1, 1, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 10, 20, 20, 20, 20, 20, 20, 8, 8, 8, 8, 8, 11, 11, 11, 8, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 10, 10, 20, 20, 20, 20, 20, 20, 8, 8, 8, 8, 16] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 127) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/127 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/127' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O) `ZINC001184249436.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184249436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184249436 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 8, 8, 4, 1, 1, 1, 1, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 10, 20, 20, 20, 20, 20, 20, 8, 8, 8, 8, 8, 11, 11, 11, 8, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 10, 10, 20, 20, 20, 20, 20, 20, 8, 8, 8, 8, 16] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 128) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/128 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/128' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O) `ZINC001184249436.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184249436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184249436 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 10, 10, 10, 5, 1, 1, 1, 1, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 18, 18, 18, 18, 18, 18, 7, 10, 10, 10, 10, 12, 12, 12, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 9, 18, 18, 18, 18, 18, 18, 7, 7, 10, 10, 20] 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, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 90 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 129) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/129 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/129' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O) `ZINC001184249436.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184249436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184249436 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 10, 10, 10, 5, 1, 1, 1, 1, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 18, 18, 18, 18, 18, 18, 7, 10, 10, 10, 10, 12, 12, 12, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 9, 18, 18, 18, 18, 18, 18, 7, 7, 10, 10, 20] 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, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 90 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184249436 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436 Building ZINC001184249436 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184249436 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 126) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O) `ZINC001184249436.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184249436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184249436 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 8, 8, 4, 1, 1, 1, 1, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 10, 20, 20, 20, 20, 20, 20, 8, 8, 8, 8, 8, 11, 11, 11, 8, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 10, 10, 20, 20, 20, 20, 20, 20, 8, 8, 8, 8, 16] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 127) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O) `ZINC001184249436.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184249436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184249436 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 8, 8, 4, 1, 1, 1, 1, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 10, 20, 20, 20, 20, 20, 20, 8, 8, 8, 8, 8, 11, 11, 11, 8, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 10, 10, 20, 20, 20, 20, 20, 20, 8, 8, 8, 8, 16] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 128) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/128: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O) `ZINC001184249436.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184249436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184249436 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 10, 10, 10, 5, 1, 1, 1, 1, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 18, 18, 18, 18, 18, 18, 7, 10, 10, 10, 10, 12, 12, 12, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 9, 18, 18, 18, 18, 18, 18, 7, 7, 10, 10, 20] 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, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 90 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 129) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/129: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O) `ZINC001184249436.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184249436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184249436 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 10, 10, 10, 5, 1, 1, 1, 1, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 18, 18, 18, 18, 18, 18, 7, 10, 10, 10, 10, 12, 12, 12, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 9, 18, 18, 18, 18, 18, 18, 7, 7, 10, 10, 20] 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, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 90 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184249436 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436 Building ZINC001184249436 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184249436 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 126) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O) `ZINC001184249436.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184249436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184249436 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 8, 8, 4, 1, 1, 1, 1, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 10, 20, 20, 20, 20, 20, 20, 8, 8, 8, 8, 8, 11, 11, 11, 8, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 10, 10, 20, 20, 20, 20, 20, 20, 8, 8, 8, 8, 16] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 127) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O) `ZINC001184249436.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184249436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184249436 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 8, 8, 4, 1, 1, 1, 1, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 10, 20, 20, 20, 20, 20, 20, 8, 8, 8, 8, 8, 11, 11, 11, 8, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 10, 10, 20, 20, 20, 20, 20, 20, 8, 8, 8, 8, 16] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 128) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/128: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O) `ZINC001184249436.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184249436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184249436 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 10, 10, 10, 5, 1, 1, 1, 1, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 18, 18, 18, 18, 18, 18, 7, 10, 10, 10, 10, 12, 12, 12, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 9, 18, 18, 18, 18, 18, 18, 7, 7, 10, 10, 20] 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, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 90 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 129) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/129: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O) `ZINC001184249436.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184249436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184249436 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 10, 10, 10, 5, 1, 1, 1, 1, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 18, 18, 18, 18, 18, 18, 7, 10, 10, 10, 10, 12, 12, 12, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 9, 18, 18, 18, 18, 18, 18, 7, 7, 10, 10, 20] 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, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 90 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184249436 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436 Building ZINC001184249436 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184249436 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 126) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O) `ZINC001184249436.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184249436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184249436 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 8, 8, 4, 1, 1, 1, 1, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 10, 20, 20, 20, 20, 20, 20, 8, 8, 8, 8, 8, 11, 11, 11, 8, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 10, 10, 20, 20, 20, 20, 20, 20, 8, 8, 8, 8, 16] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 127) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O) `ZINC001184249436.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184249436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184249436 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 8, 8, 4, 1, 1, 1, 1, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 10, 20, 20, 20, 20, 20, 20, 8, 8, 8, 8, 8, 11, 11, 11, 8, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 10, 10, 20, 20, 20, 20, 20, 20, 8, 8, 8, 8, 16] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 128) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/128: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O) `ZINC001184249436.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184249436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184249436 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 10, 10, 10, 5, 1, 1, 1, 1, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 18, 18, 18, 18, 18, 18, 7, 10, 10, 10, 10, 12, 12, 12, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 9, 18, 18, 18, 18, 18, 18, 7, 7, 10, 10, 20] 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, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 90 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 129) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/129: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O) `ZINC001184249436.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184249436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184249436 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC[C@]3(C2)COCCN(Cc2c(C)noc2C)C3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 10, 5, 1, 1, 5, 8, 12, 1, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 10, 10, 10, 5, 1, 1, 1, 1, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 18, 18, 18, 18, 18, 18, 7, 10, 10, 10, 10, 12, 12, 12, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 9, 18, 18, 18, 18, 18, 18, 7, 7, 10, 10, 20] 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, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 90 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184249436 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249436 Building ZINC001184249492 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184249492 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 130) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/130 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/130' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@@H]3CN(Cc4csc(C)n4)CCO[C@@H]3C2)ccc1O) `ZINC001184249492.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184249492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184249492 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@@H]3CN(Cc4csc(C)n4)CCO[C@@H]3C2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 1, 1, 14, 1, 5, 8, 5, 5, 12, 5, 7, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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: [16, 10, 10, 10, 5, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 8, 8, 8, 15, 20, 20, 20, 20, 20, 8, 8, 8, 8, 8, 8, 10, 10, 10, 10, 16, 16, 16, 10, 5, 5, 8, 8, 8, 8, 8, 8, 15, 15, 20, 20, 20, 20, 8, 8, 8, 8, 8, 8, 10, 10, 20] 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, 60]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 131) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/131 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/131' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@@H]3CN(Cc4csc(C)n4)CCO[C@@H]3C2)ccc1O) `ZINC001184249492.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184249492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184249492 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@@H]3CN(Cc4csc(C)n4)CCO[C@@H]3C2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 1, 1, 14, 1, 5, 8, 5, 5, 12, 5, 7, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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: [16, 10, 10, 10, 5, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 8, 8, 8, 15, 20, 20, 20, 20, 20, 8, 8, 8, 8, 8, 8, 10, 10, 10, 10, 16, 16, 16, 10, 5, 5, 8, 8, 8, 8, 8, 8, 15, 15, 20, 20, 20, 20, 8, 8, 8, 8, 8, 8, 10, 10, 20] 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, 60]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 132) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/132 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/132' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@@H]3CN(Cc4csc(C)n4)CCO[C@@H]3C2)ccc1O) `ZINC001184249492.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184249492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184249492 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@@H]3CN(Cc4csc(C)n4)CCO[C@@H]3C2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 1, 1, 14, 1, 5, 8, 5, 5, 12, 5, 7, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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: [16, 9, 9, 9, 5, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 5, 5, 5, 13, 24, 24, 24, 24, 24, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 16, 16, 16, 9, 5, 5, 5, 5, 5, 5, 5, 5, 13, 13, 24, 24, 24, 24, 5, 5, 5, 5, 5, 5, 9, 9, 18] 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, 60]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 133) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/133 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/133' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@@H]3CN(Cc4csc(C)n4)CCO[C@@H]3C2)ccc1O) `ZINC001184249492.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184249492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184249492 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@@H]3CN(Cc4csc(C)n4)CCO[C@@H]3C2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 1, 1, 14, 1, 5, 8, 5, 5, 12, 5, 7, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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: [16, 9, 9, 9, 5, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 5, 5, 5, 13, 24, 24, 24, 24, 24, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 16, 16, 16, 9, 5, 5, 5, 5, 5, 5, 5, 5, 13, 13, 24, 24, 24, 24, 5, 5, 5, 5, 5, 5, 9, 9, 18] 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, 60]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184249492 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492 Building ZINC001184249492 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184249492 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 130) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@@H]3CN(Cc4csc(C)n4)CCO[C@@H]3C2)ccc1O) `ZINC001184249492.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184249492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184249492 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@@H]3CN(Cc4csc(C)n4)CCO[C@@H]3C2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 1, 1, 14, 1, 5, 8, 5, 5, 12, 5, 7, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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: [16, 10, 10, 10, 5, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 8, 8, 8, 15, 20, 20, 20, 20, 20, 8, 8, 8, 8, 8, 8, 10, 10, 10, 10, 16, 16, 16, 10, 5, 5, 8, 8, 8, 8, 8, 8, 15, 15, 20, 20, 20, 20, 8, 8, 8, 8, 8, 8, 10, 10, 20] 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, 60]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 131) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@@H]3CN(Cc4csc(C)n4)CCO[C@@H]3C2)ccc1O) `ZINC001184249492.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184249492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184249492 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@@H]3CN(Cc4csc(C)n4)CCO[C@@H]3C2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 1, 1, 14, 1, 5, 8, 5, 5, 12, 5, 7, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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: [16, 10, 10, 10, 5, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 8, 8, 8, 15, 20, 20, 20, 20, 20, 8, 8, 8, 8, 8, 8, 10, 10, 10, 10, 16, 16, 16, 10, 5, 5, 8, 8, 8, 8, 8, 8, 15, 15, 20, 20, 20, 20, 8, 8, 8, 8, 8, 8, 10, 10, 20] 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, 60]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 132) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/132: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CC[C@@H]3CN(Cc4csc(C)n4)CCO[C@@H]3C2)ccc1O) `ZINC001184249492.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184249492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184249492 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@@H]3CN(Cc4csc(C)n4)CCO[C@@H]3C2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 1, 1, 14, 1, 5, 8, 5, 5, 12, 5, 7, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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: [16, 9, 9, 9, 5, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 5, 5, 5, 13, 24, 24, 24, 24, 24, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 16, 16, 16, 9, 5, 5, 5, 5, 5, 5, 5, 5, 13, 13, 24, 24, 24, 24, 5, 5, 5, 5, 5, 5, 9, 9, 18] 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, 60]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 133) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/133: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CC[C@@H]3CN(Cc4csc(C)n4)CCO[C@@H]3C2)ccc1O) `ZINC001184249492.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184249492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184249492 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@@H]3CN(Cc4csc(C)n4)CCO[C@@H]3C2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 1, 1, 14, 1, 5, 8, 5, 5, 12, 5, 7, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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: [16, 9, 9, 9, 5, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 5, 5, 5, 13, 24, 24, 24, 24, 24, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 16, 16, 16, 9, 5, 5, 5, 5, 5, 5, 5, 5, 13, 13, 24, 24, 24, 24, 5, 5, 5, 5, 5, 5, 9, 9, 18] 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, 60]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184249492 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492 Building ZINC001184249492 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184249492 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 130) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@@H]3CN(Cc4csc(C)n4)CCO[C@@H]3C2)ccc1O) `ZINC001184249492.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184249492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184249492 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@@H]3CN(Cc4csc(C)n4)CCO[C@@H]3C2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 1, 1, 14, 1, 5, 8, 5, 5, 12, 5, 7, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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: [16, 10, 10, 10, 5, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 8, 8, 8, 15, 20, 20, 20, 20, 20, 8, 8, 8, 8, 8, 8, 10, 10, 10, 10, 16, 16, 16, 10, 5, 5, 8, 8, 8, 8, 8, 8, 15, 15, 20, 20, 20, 20, 8, 8, 8, 8, 8, 8, 10, 10, 20] 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, 60]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 131) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@@H]3CN(Cc4csc(C)n4)CCO[C@@H]3C2)ccc1O) `ZINC001184249492.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184249492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184249492 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@@H]3CN(Cc4csc(C)n4)CCO[C@@H]3C2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 1, 1, 14, 1, 5, 8, 5, 5, 12, 5, 7, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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: [16, 10, 10, 10, 5, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 8, 8, 8, 15, 20, 20, 20, 20, 20, 8, 8, 8, 8, 8, 8, 10, 10, 10, 10, 16, 16, 16, 10, 5, 5, 8, 8, 8, 8, 8, 8, 15, 15, 20, 20, 20, 20, 8, 8, 8, 8, 8, 8, 10, 10, 20] 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, 60]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 132) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/132: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CC[C@@H]3CN(Cc4csc(C)n4)CCO[C@@H]3C2)ccc1O) `ZINC001184249492.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184249492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184249492 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@@H]3CN(Cc4csc(C)n4)CCO[C@@H]3C2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 1, 1, 14, 1, 5, 8, 5, 5, 12, 5, 7, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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: [16, 9, 9, 9, 5, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 5, 5, 5, 13, 24, 24, 24, 24, 24, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 16, 16, 16, 9, 5, 5, 5, 5, 5, 5, 5, 5, 13, 13, 24, 24, 24, 24, 5, 5, 5, 5, 5, 5, 9, 9, 18] 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, 60]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 133) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/133: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CC[C@@H]3CN(Cc4csc(C)n4)CCO[C@@H]3C2)ccc1O) `ZINC001184249492.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184249492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184249492 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@@H]3CN(Cc4csc(C)n4)CCO[C@@H]3C2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 1, 1, 14, 1, 5, 8, 5, 5, 12, 5, 7, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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: [16, 9, 9, 9, 5, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 5, 5, 5, 13, 24, 24, 24, 24, 24, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 16, 16, 16, 9, 5, 5, 5, 5, 5, 5, 5, 5, 13, 13, 24, 24, 24, 24, 5, 5, 5, 5, 5, 5, 9, 9, 18] 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, 60]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184249492 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492 Building ZINC001184249492 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184249492 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 130) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@@H]3CN(Cc4csc(C)n4)CCO[C@@H]3C2)ccc1O) `ZINC001184249492.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184249492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184249492 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@@H]3CN(Cc4csc(C)n4)CCO[C@@H]3C2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 1, 1, 14, 1, 5, 8, 5, 5, 12, 5, 7, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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: [16, 10, 10, 10, 5, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 8, 8, 8, 15, 20, 20, 20, 20, 20, 8, 8, 8, 8, 8, 8, 10, 10, 10, 10, 16, 16, 16, 10, 5, 5, 8, 8, 8, 8, 8, 8, 15, 15, 20, 20, 20, 20, 8, 8, 8, 8, 8, 8, 10, 10, 20] 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, 60]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 131) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@@H]3CN(Cc4csc(C)n4)CCO[C@@H]3C2)ccc1O) `ZINC001184249492.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184249492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184249492 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@@H]3CN(Cc4csc(C)n4)CCO[C@@H]3C2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 1, 1, 14, 1, 5, 8, 5, 5, 12, 5, 7, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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: [16, 10, 10, 10, 5, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 8, 8, 8, 15, 20, 20, 20, 20, 20, 8, 8, 8, 8, 8, 8, 10, 10, 10, 10, 16, 16, 16, 10, 5, 5, 8, 8, 8, 8, 8, 8, 15, 15, 20, 20, 20, 20, 8, 8, 8, 8, 8, 8, 10, 10, 20] 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, 60]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 132) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/132: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CC[C@@H]3CN(Cc4csc(C)n4)CCO[C@@H]3C2)ccc1O) `ZINC001184249492.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184249492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184249492 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@@H]3CN(Cc4csc(C)n4)CCO[C@@H]3C2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 1, 1, 14, 1, 5, 8, 5, 5, 12, 5, 7, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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: [16, 9, 9, 9, 5, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 5, 5, 5, 13, 24, 24, 24, 24, 24, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 16, 16, 16, 9, 5, 5, 5, 5, 5, 5, 5, 5, 13, 13, 24, 24, 24, 24, 5, 5, 5, 5, 5, 5, 9, 9, 18] 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, 60]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 133) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/133: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CC[C@@H]3CN(Cc4csc(C)n4)CCO[C@@H]3C2)ccc1O) `ZINC001184249492.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184249492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184249492 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@@H]3CN(Cc4csc(C)n4)CCO[C@@H]3C2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 1, 1, 14, 1, 5, 8, 5, 5, 12, 5, 7, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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: [16, 9, 9, 9, 5, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 5, 5, 5, 13, 24, 24, 24, 24, 24, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 16, 16, 16, 9, 5, 5, 5, 5, 5, 5, 5, 5, 13, 13, 24, 24, 24, 24, 5, 5, 5, 5, 5, 5, 9, 9, 18] 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, 60]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184249492 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249492 Building ZINC001184249511 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249511' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249511 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184249511 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249511/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249511 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 134) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/134 `/scratch/xiaobo/418326/xbt-8058088.46/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)N2CCC3(CCC(=O)N3Cc3csc(C)n3)CC2)ccc1O) `ZINC001184249511.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184249511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184249511 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC3(CCC(=O)N3Cc3csc(C)n3)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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 14, 1, 5, 8, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [19, 10, 10, 10, 5, 1, 1, 1, 2, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 22, 22, 22, 22, 22, 5, 5, 10, 10, 10, 10, 19, 19, 19, 10, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 22, 22, 22, 22, 5, 5, 5, 5, 10, 10, 20] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 108 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249511 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249511/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249511 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 135) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/135 `/scratch/xiaobo/418326/xbt-8058088.46/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)N2CCC3(CCC(=O)N3Cc3csc(C)n3)CC2)ccc1O) `ZINC001184249511.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184249511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249511/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184249511 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC3(CCC(=O)N3Cc3csc(C)n3)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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 14, 1, 5, 8, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [14, 8, 8, 8, 4, 1, 1, 1, 1, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12, 21, 21, 21, 21, 21, 8, 8, 8, 8, 8, 8, 14, 14, 14, 8, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 21, 21, 21, 21, 8, 8, 8, 8, 8, 8, 16] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249511 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184249511 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249511/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249511/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249511 Building ZINC001184249511 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249511' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249511 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184249511 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249511/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249511 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 134) grep: /scratch/xiaobo/418326/xbt-8058088.46/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)N2CCC3(CCC(=O)N3Cc3csc(C)n3)CC2)ccc1O) `ZINC001184249511.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184249511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184249511 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC3(CCC(=O)N3Cc3csc(C)n3)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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 14, 1, 5, 8, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [19, 10, 10, 10, 5, 1, 1, 1, 2, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 22, 22, 22, 22, 22, 5, 5, 10, 10, 10, 10, 19, 19, 19, 10, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 22, 22, 22, 22, 5, 5, 5, 5, 10, 10, 20] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 108 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249511 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249511/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249511 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 135) grep: /scratch/xiaobo/418326/xbt-8058088.46/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)N2CCC3(CCC(=O)N3Cc3csc(C)n3)CC2)ccc1O) `ZINC001184249511.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184249511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249511/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184249511 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC3(CCC(=O)N3Cc3csc(C)n3)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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 14, 1, 5, 8, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [14, 8, 8, 8, 4, 1, 1, 1, 1, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12, 21, 21, 21, 21, 21, 8, 8, 8, 8, 8, 8, 14, 14, 14, 8, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 21, 21, 21, 21, 8, 8, 8, 8, 8, 8, 16] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249511 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184249511 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249511/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249511/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249511 Building ZINC001184249634 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249634' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249634 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184249634 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249634/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249634 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 136) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/136 `/scratch/xiaobo/418326/xbt-8058088.46/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)N2CCC3(CCn4c(c5ccc(C(N)=O)cc5)cnc43)CC2)ccc1O) `ZINC001184249634.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184249634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184249634 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC3(CCn4c(c5ccc(C(N)=O)cc5)cnc43)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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', '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, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 11, 1, 1, 1, 8, 1, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 10, 10, 10, 5, 1, 1, 1, 2, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 15, 25, 25, 15, 15, 5, 5, 5, 5, 5, 10, 10, 10, 10, 17, 17, 17, 10, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 15, 25, 25, 15, 15, 5, 5, 5, 5, 5, 10, 10, 20] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249634 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249634/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249634 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 137) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/137 `/scratch/xiaobo/418326/xbt-8058088.46/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)N2CCC3(CCn4c(c5ccc(C(N)=O)cc5)cnc43)CC2)ccc1O) `ZINC001184249634.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184249634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249634/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184249634 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC3(CCn4c(c5ccc(C(N)=O)cc5)cnc43)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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', '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, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 11, 1, 1, 1, 8, 1, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 10, 10, 10, 5, 1, 1, 1, 2, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 16, 16, 16, 26, 26, 16, 16, 5, 5, 5, 5, 5, 10, 10, 10, 10, 16, 16, 16, 10, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 16, 26, 26, 16, 16, 5, 5, 5, 5, 5, 10, 10, 20] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249634 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184249634 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249634/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249634/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249634 Building ZINC001184249634 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249634' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249634 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184249634 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249634/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249634 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 136) grep: /scratch/xiaobo/418326/xbt-8058088.46/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)N2CCC3(CCn4c(c5ccc(C(N)=O)cc5)cnc43)CC2)ccc1O) `ZINC001184249634.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184249634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184249634 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC3(CCn4c(c5ccc(C(N)=O)cc5)cnc43)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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', '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, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 11, 1, 1, 1, 8, 1, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 10, 10, 10, 5, 1, 1, 1, 2, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 15, 25, 25, 15, 15, 5, 5, 5, 5, 5, 10, 10, 10, 10, 17, 17, 17, 10, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 15, 25, 25, 15, 15, 5, 5, 5, 5, 5, 10, 10, 20] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249634 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249634/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249634 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 137) grep: /scratch/xiaobo/418326/xbt-8058088.46/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)N2CCC3(CCn4c(c5ccc(C(N)=O)cc5)cnc43)CC2)ccc1O) `ZINC001184249634.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184249634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249634/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184249634 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC3(CCn4c(c5ccc(C(N)=O)cc5)cnc43)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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', '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, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 11, 1, 1, 1, 8, 1, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 10, 10, 10, 5, 1, 1, 1, 2, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 16, 16, 16, 26, 26, 16, 16, 5, 5, 5, 5, 5, 10, 10, 10, 10, 16, 16, 16, 10, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 16, 26, 26, 16, 16, 5, 5, 5, 5, 5, 10, 10, 20] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249634 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184249634 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249634/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249634/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249634 Building ZINC001184249816 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184249816 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 138) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/138 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/138' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C)c1nc(C2CCN(C(=O)[C@@]([O-])([SiH3])Cc3ccc(O)c(OC)c3)CC2)cc2c1ncn2C) `ZINC001184249816.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184249816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001184249816 none COCCN(C)c1nc(C2CCN(C(=O)[C@@]([O-])([SiH3])Cc3ccc(O)c(OC)c3)CC2)cc2c1ncn2C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 5, 1, 1, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [28, 28, 28, 24, 12, 24, 12, 12, 4, 4, 4, 4, 2, 1, 3, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 10, 9, 4, 4, 12, 12, 12, 12, 12, 12, 12, 28, 28, 28, 28, 28, 28, 28, 24, 24, 24, 4, 4, 4, 4, 4, 5, 5, 9, 9, 18, 10, 10, 10, 9, 4, 4, 4, 4, 12, 12, 12, 12, 12] 100 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 139) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/139 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/139' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C)c1nc(C2CCN(C(=O)[C@@]([O-])([SiH3])Cc3ccc(O)c(OC)c3)CC2)cc2c1ncn2C) `ZINC001184249816.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184249816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001184249816 none COCCN(C)c1nc(C2CCN(C(=O)[C@@]([O-])([SiH3])Cc3ccc(O)c(OC)c3)CC2)cc2c1ncn2C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 5, 1, 1, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [28, 28, 28, 24, 12, 24, 12, 12, 4, 4, 4, 4, 2, 1, 3, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 10, 9, 4, 4, 12, 12, 12, 12, 12, 12, 12, 28, 28, 28, 28, 28, 28, 28, 24, 24, 24, 4, 4, 4, 4, 4, 5, 5, 9, 9, 18, 10, 10, 10, 9, 4, 4, 4, 4, 12, 12, 12, 12, 12] 100 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 140) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/140 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/140' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C)c1nc(C2CCN(C(=O)[C@]([O-])([SiH3])Cc3ccc(O)c(OC)c3)CC2)cc2c1ncn2C) `ZINC001184249816.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184249816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001184249816 none COCCN(C)c1nc(C2CCN(C(=O)[C@]([O-])([SiH3])Cc3ccc(O)c(OC)c3)CC2)cc2c1ncn2C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 5, 1, 1, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [29, 27, 25, 22, 7, 22, 7, 7, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 3, 5, 5, 5, 5, 5, 5, 11, 5, 2, 2, 7, 7, 7, 7, 7, 7, 7, 29, 29, 29, 27, 27, 25, 25, 22, 22, 22, 2, 2, 2, 2, 2, 3, 3, 5, 5, 10, 11, 11, 11, 5, 2, 2, 2, 2, 7, 7, 7, 7, 7] 100 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 141) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/141 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/141' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C)c1nc(C2CCN(C(=O)[C@]([O-])([SiH3])Cc3ccc(O)c(OC)c3)CC2)cc2c1ncn2C) `ZINC001184249816.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184249816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001184249816 none COCCN(C)c1nc(C2CCN(C(=O)[C@]([O-])([SiH3])Cc3ccc(O)c(OC)c3)CC2)cc2c1ncn2C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 5, 1, 1, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [29, 27, 25, 22, 7, 22, 7, 7, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 3, 5, 5, 5, 5, 5, 5, 11, 5, 2, 2, 7, 7, 7, 7, 7, 7, 7, 29, 29, 29, 27, 27, 25, 25, 22, 22, 22, 2, 2, 2, 2, 2, 3, 3, 5, 5, 10, 11, 11, 11, 5, 2, 2, 2, 2, 7, 7, 7, 7, 7] 100 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184249816 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816 Building ZINC001184249816 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184249816 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 138) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COCCN(C)c1nc(C2CCN(C(=O)[C@@]([O-])([SiH3])Cc3ccc(O)c(OC)c3)CC2)cc2c1ncn2C) `ZINC001184249816.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184249816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001184249816 none COCCN(C)c1nc(C2CCN(C(=O)[C@@]([O-])([SiH3])Cc3ccc(O)c(OC)c3)CC2)cc2c1ncn2C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 5, 1, 1, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [28, 28, 28, 24, 12, 24, 12, 12, 4, 4, 4, 4, 2, 1, 3, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 10, 9, 4, 4, 12, 12, 12, 12, 12, 12, 12, 28, 28, 28, 28, 28, 28, 28, 24, 24, 24, 4, 4, 4, 4, 4, 5, 5, 9, 9, 18, 10, 10, 10, 9, 4, 4, 4, 4, 12, 12, 12, 12, 12] 100 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 139) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COCCN(C)c1nc(C2CCN(C(=O)[C@@]([O-])([SiH3])Cc3ccc(O)c(OC)c3)CC2)cc2c1ncn2C) `ZINC001184249816.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184249816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001184249816 none COCCN(C)c1nc(C2CCN(C(=O)[C@@]([O-])([SiH3])Cc3ccc(O)c(OC)c3)CC2)cc2c1ncn2C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 5, 1, 1, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [28, 28, 28, 24, 12, 24, 12, 12, 4, 4, 4, 4, 2, 1, 3, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 10, 9, 4, 4, 12, 12, 12, 12, 12, 12, 12, 28, 28, 28, 28, 28, 28, 28, 24, 24, 24, 4, 4, 4, 4, 4, 5, 5, 9, 9, 18, 10, 10, 10, 9, 4, 4, 4, 4, 12, 12, 12, 12, 12] 100 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 140) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/140: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1nc(C2CCN(C(=O)[C@]([O-])([SiH3])Cc3ccc(O)c(OC)c3)CC2)cc2c1ncn2C) `ZINC001184249816.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184249816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001184249816 none COCCN(C)c1nc(C2CCN(C(=O)[C@]([O-])([SiH3])Cc3ccc(O)c(OC)c3)CC2)cc2c1ncn2C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 5, 1, 1, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [29, 27, 25, 22, 7, 22, 7, 7, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 3, 5, 5, 5, 5, 5, 5, 11, 5, 2, 2, 7, 7, 7, 7, 7, 7, 7, 29, 29, 29, 27, 27, 25, 25, 22, 22, 22, 2, 2, 2, 2, 2, 3, 3, 5, 5, 10, 11, 11, 11, 5, 2, 2, 2, 2, 7, 7, 7, 7, 7] 100 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 141) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/141: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1nc(C2CCN(C(=O)[C@]([O-])([SiH3])Cc3ccc(O)c(OC)c3)CC2)cc2c1ncn2C) `ZINC001184249816.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184249816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001184249816 none COCCN(C)c1nc(C2CCN(C(=O)[C@]([O-])([SiH3])Cc3ccc(O)c(OC)c3)CC2)cc2c1ncn2C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 5, 1, 1, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [29, 27, 25, 22, 7, 22, 7, 7, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 3, 5, 5, 5, 5, 5, 5, 11, 5, 2, 2, 7, 7, 7, 7, 7, 7, 7, 29, 29, 29, 27, 27, 25, 25, 22, 22, 22, 2, 2, 2, 2, 2, 3, 3, 5, 5, 10, 11, 11, 11, 5, 2, 2, 2, 2, 7, 7, 7, 7, 7] 100 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184249816 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816 Building ZINC001184249816 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184249816 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 138) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COCCN(C)c1nc(C2CCN(C(=O)[C@@]([O-])([SiH3])Cc3ccc(O)c(OC)c3)CC2)cc2c1ncn2C) `ZINC001184249816.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184249816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001184249816 none COCCN(C)c1nc(C2CCN(C(=O)[C@@]([O-])([SiH3])Cc3ccc(O)c(OC)c3)CC2)cc2c1ncn2C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 5, 1, 1, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [28, 28, 28, 24, 12, 24, 12, 12, 4, 4, 4, 4, 2, 1, 3, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 10, 9, 4, 4, 12, 12, 12, 12, 12, 12, 12, 28, 28, 28, 28, 28, 28, 28, 24, 24, 24, 4, 4, 4, 4, 4, 5, 5, 9, 9, 18, 10, 10, 10, 9, 4, 4, 4, 4, 12, 12, 12, 12, 12] 100 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 139) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COCCN(C)c1nc(C2CCN(C(=O)[C@@]([O-])([SiH3])Cc3ccc(O)c(OC)c3)CC2)cc2c1ncn2C) `ZINC001184249816.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184249816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001184249816 none COCCN(C)c1nc(C2CCN(C(=O)[C@@]([O-])([SiH3])Cc3ccc(O)c(OC)c3)CC2)cc2c1ncn2C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 5, 1, 1, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [28, 28, 28, 24, 12, 24, 12, 12, 4, 4, 4, 4, 2, 1, 3, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 10, 9, 4, 4, 12, 12, 12, 12, 12, 12, 12, 28, 28, 28, 28, 28, 28, 28, 24, 24, 24, 4, 4, 4, 4, 4, 5, 5, 9, 9, 18, 10, 10, 10, 9, 4, 4, 4, 4, 12, 12, 12, 12, 12] 100 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 140) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/140: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1nc(C2CCN(C(=O)[C@]([O-])([SiH3])Cc3ccc(O)c(OC)c3)CC2)cc2c1ncn2C) `ZINC001184249816.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184249816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001184249816 none COCCN(C)c1nc(C2CCN(C(=O)[C@]([O-])([SiH3])Cc3ccc(O)c(OC)c3)CC2)cc2c1ncn2C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 5, 1, 1, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [29, 27, 25, 22, 7, 22, 7, 7, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 3, 5, 5, 5, 5, 5, 5, 11, 5, 2, 2, 7, 7, 7, 7, 7, 7, 7, 29, 29, 29, 27, 27, 25, 25, 22, 22, 22, 2, 2, 2, 2, 2, 3, 3, 5, 5, 10, 11, 11, 11, 5, 2, 2, 2, 2, 7, 7, 7, 7, 7] 100 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 141) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/141: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1nc(C2CCN(C(=O)[C@]([O-])([SiH3])Cc3ccc(O)c(OC)c3)CC2)cc2c1ncn2C) `ZINC001184249816.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184249816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001184249816 none COCCN(C)c1nc(C2CCN(C(=O)[C@]([O-])([SiH3])Cc3ccc(O)c(OC)c3)CC2)cc2c1ncn2C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 5, 1, 1, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [29, 27, 25, 22, 7, 22, 7, 7, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 3, 5, 5, 5, 5, 5, 5, 11, 5, 2, 2, 7, 7, 7, 7, 7, 7, 7, 29, 29, 29, 27, 27, 25, 25, 22, 22, 22, 2, 2, 2, 2, 2, 3, 3, 5, 5, 10, 11, 11, 11, 5, 2, 2, 2, 2, 7, 7, 7, 7, 7] 100 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184249816 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816 Building ZINC001184249816 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184249816 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 138) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COCCN(C)c1nc(C2CCN(C(=O)[C@@]([O-])([SiH3])Cc3ccc(O)c(OC)c3)CC2)cc2c1ncn2C) `ZINC001184249816.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184249816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001184249816 none COCCN(C)c1nc(C2CCN(C(=O)[C@@]([O-])([SiH3])Cc3ccc(O)c(OC)c3)CC2)cc2c1ncn2C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 5, 1, 1, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [28, 28, 28, 24, 12, 24, 12, 12, 4, 4, 4, 4, 2, 1, 3, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 10, 9, 4, 4, 12, 12, 12, 12, 12, 12, 12, 28, 28, 28, 28, 28, 28, 28, 24, 24, 24, 4, 4, 4, 4, 4, 5, 5, 9, 9, 18, 10, 10, 10, 9, 4, 4, 4, 4, 12, 12, 12, 12, 12] 100 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 139) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COCCN(C)c1nc(C2CCN(C(=O)[C@@]([O-])([SiH3])Cc3ccc(O)c(OC)c3)CC2)cc2c1ncn2C) `ZINC001184249816.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184249816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001184249816 none COCCN(C)c1nc(C2CCN(C(=O)[C@@]([O-])([SiH3])Cc3ccc(O)c(OC)c3)CC2)cc2c1ncn2C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 5, 1, 1, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [28, 28, 28, 24, 12, 24, 12, 12, 4, 4, 4, 4, 2, 1, 3, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 10, 9, 4, 4, 12, 12, 12, 12, 12, 12, 12, 28, 28, 28, 28, 28, 28, 28, 24, 24, 24, 4, 4, 4, 4, 4, 5, 5, 9, 9, 18, 10, 10, 10, 9, 4, 4, 4, 4, 12, 12, 12, 12, 12] 100 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 140) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/140: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1nc(C2CCN(C(=O)[C@]([O-])([SiH3])Cc3ccc(O)c(OC)c3)CC2)cc2c1ncn2C) `ZINC001184249816.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184249816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001184249816 none COCCN(C)c1nc(C2CCN(C(=O)[C@]([O-])([SiH3])Cc3ccc(O)c(OC)c3)CC2)cc2c1ncn2C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 5, 1, 1, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [29, 27, 25, 22, 7, 22, 7, 7, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 3, 5, 5, 5, 5, 5, 5, 11, 5, 2, 2, 7, 7, 7, 7, 7, 7, 7, 29, 29, 29, 27, 27, 25, 25, 22, 22, 22, 2, 2, 2, 2, 2, 3, 3, 5, 5, 10, 11, 11, 11, 5, 2, 2, 2, 2, 7, 7, 7, 7, 7] 100 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 141) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/141: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1nc(C2CCN(C(=O)[C@]([O-])([SiH3])Cc3ccc(O)c(OC)c3)CC2)cc2c1ncn2C) `ZINC001184249816.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184249816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC001184249816 none COCCN(C)c1nc(C2CCN(C(=O)[C@]([O-])([SiH3])Cc3ccc(O)c(OC)c3)CC2)cc2c1ncn2C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 5, 1, 1, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [29, 27, 25, 22, 7, 22, 7, 7, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 3, 5, 5, 5, 5, 5, 5, 11, 5, 2, 2, 7, 7, 7, 7, 7, 7, 7, 29, 29, 29, 27, 27, 25, 25, 22, 22, 22, 2, 2, 2, 2, 2, 3, 3, 5, 5, 10, 11, 11, 11, 5, 2, 2, 2, 2, 7, 7, 7, 7, 7] 100 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184249816 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184249816 Building ZINC001184250497 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184250497' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184250497 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184250497 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184250497/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184250497 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 142) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/142 `/scratch/xiaobo/418326/xbt-8058088.46/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)N2CC[C@]3(CC[C@@H](C(=O)Nc4cccnc4)O3)[C@@H](C)C2)ccc1O) `ZINC001184250497.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184250497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184250497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184250497 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@]3(CC[C@@H](C(=O)Nc4cccnc4)O3)[C@@H](C)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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 1, 12, 5, 7, 5, 5, 1, 1, 1, 12, 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, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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: [16, 9, 9, 9, 5, 1, 1, 1, 2, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 11, 11, 11, 22, 22, 22, 22, 22, 7, 7, 7, 7, 7, 9, 9, 9, 9, 16, 16, 16, 9, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 11, 22, 22, 22, 22, 7, 7, 7, 7, 7, 9, 9, 18] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 95 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184250497 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184250497/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184250497 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 143) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/143 `/scratch/xiaobo/418326/xbt-8058088.46/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)N2CC[C@]3(CC[C@@H](C(=O)Nc4cccnc4)O3)[C@@H](C)C2)ccc1O) `ZINC001184250497.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184250497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184250497/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184250497 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@]3(CC[C@@H](C(=O)Nc4cccnc4)O3)[C@@H](C)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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 1, 12, 5, 7, 5, 5, 1, 1, 1, 12, 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, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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, 9, 9, 5, 1, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 18, 18, 18, 18, 18, 6, 6, 6, 6, 6, 9, 9, 9, 9, 15, 15, 15, 9, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 10, 18, 18, 18, 18, 6, 6, 6, 6, 6, 9, 9, 18] 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, 60, 61, 62]) total number of confs: 89 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184250497 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184250497 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184250497/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184250497/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184250497 Building ZINC001184250497 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184250497' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184250497 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184250497 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184250497/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184250497 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 142) grep: /scratch/xiaobo/418326/xbt-8058088.46/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)N2CC[C@]3(CC[C@@H](C(=O)Nc4cccnc4)O3)[C@@H](C)C2)ccc1O) `ZINC001184250497.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184250497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184250497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184250497 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@]3(CC[C@@H](C(=O)Nc4cccnc4)O3)[C@@H](C)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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 1, 12, 5, 7, 5, 5, 1, 1, 1, 12, 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, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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: [16, 9, 9, 9, 5, 1, 1, 1, 2, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 11, 11, 11, 22, 22, 22, 22, 22, 7, 7, 7, 7, 7, 9, 9, 9, 9, 16, 16, 16, 9, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 11, 22, 22, 22, 22, 7, 7, 7, 7, 7, 9, 9, 18] 100 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 95 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184250497 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184250497/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184250497 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 143) grep: /scratch/xiaobo/418326/xbt-8058088.46/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)N2CC[C@]3(CC[C@@H](C(=O)Nc4cccnc4)O3)[C@@H](C)C2)ccc1O) `ZINC001184250497.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184250497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184250497/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184250497 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@]3(CC[C@@H](C(=O)Nc4cccnc4)O3)[C@@H](C)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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 1, 12, 5, 7, 5, 5, 1, 1, 1, 12, 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, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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, 9, 9, 5, 1, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 18, 18, 18, 18, 18, 6, 6, 6, 6, 6, 9, 9, 9, 9, 15, 15, 15, 9, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 10, 18, 18, 18, 18, 6, 6, 6, 6, 6, 9, 9, 18] 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, 60, 61, 62]) total number of confs: 89 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184250497 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184250497 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184250497/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184250497/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184250497 Building ZINC001184250499 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184250499' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184250499 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184250499 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184250499/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184250499 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 144) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/144 `/scratch/xiaobo/418326/xbt-8058088.46/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)N2CC[C@]3(CC[C@H](C(=O)Nc4cccnc4)O3)[C@@H](C)C2)ccc1O) `ZINC001184250499.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184250499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184250499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184250499 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@]3(CC[C@H](C(=O)Nc4cccnc4)O3)[C@@H](C)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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 1, 12, 5, 7, 5, 5, 1, 1, 1, 12, 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, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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: [13, 9, 9, 9, 5, 1, 1, 1, 1, 2, 5, 7, 7, 7, 7, 7, 7, 7, 7, 12, 12, 12, 26, 26, 26, 26, 26, 7, 7, 7, 7, 7, 9, 9, 9, 9, 13, 13, 13, 9, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 12, 26, 26, 26, 26, 7, 7, 7, 7, 7, 9, 9, 18] 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, 60, 61, 62]) total number of confs: 103 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184250499 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184250499/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184250499 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 145) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/145 `/scratch/xiaobo/418326/xbt-8058088.46/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)N2CC[C@]3(CC[C@H](C(=O)Nc4cccnc4)O3)[C@@H](C)C2)ccc1O) `ZINC001184250499.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184250499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184250499/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184250499 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@]3(CC[C@H](C(=O)Nc4cccnc4)O3)[C@@H](C)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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 1, 12, 5, 7, 5, 5, 1, 1, 1, 12, 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, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 6, 3, 1, 1, 1, 1, 2, 4, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 25, 25, 25, 25, 25, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 6, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 10, 25, 25, 25, 25, 6, 6, 6, 6, 6, 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, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184250499 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184250499 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184250499/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184250499/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184250499 Building ZINC001184250499 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184250499' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184250499 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184250499 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184250499/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184250499 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 144) grep: /scratch/xiaobo/418326/xbt-8058088.46/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)N2CC[C@]3(CC[C@H](C(=O)Nc4cccnc4)O3)[C@@H](C)C2)ccc1O) `ZINC001184250499.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184250499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184250499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184250499 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@]3(CC[C@H](C(=O)Nc4cccnc4)O3)[C@@H](C)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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 1, 12, 5, 7, 5, 5, 1, 1, 1, 12, 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, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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: [13, 9, 9, 9, 5, 1, 1, 1, 1, 2, 5, 7, 7, 7, 7, 7, 7, 7, 7, 12, 12, 12, 26, 26, 26, 26, 26, 7, 7, 7, 7, 7, 9, 9, 9, 9, 13, 13, 13, 9, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 12, 26, 26, 26, 26, 7, 7, 7, 7, 7, 9, 9, 18] 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, 60, 61, 62]) total number of confs: 103 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184250499 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184250499/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184250499 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 145) grep: /scratch/xiaobo/418326/xbt-8058088.46/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)N2CC[C@]3(CC[C@H](C(=O)Nc4cccnc4)O3)[C@@H](C)C2)ccc1O) `ZINC001184250499.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184250499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184250499/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184250499 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@]3(CC[C@H](C(=O)Nc4cccnc4)O3)[C@@H](C)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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 1, 12, 5, 7, 5, 5, 1, 1, 1, 12, 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, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 6, 3, 1, 1, 1, 1, 2, 4, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 25, 25, 25, 25, 25, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 6, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 10, 25, 25, 25, 25, 6, 6, 6, 6, 6, 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, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184250499 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184250499 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184250499/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184250499/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184250499 Building ZINC001184252152 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184252152 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 146) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/146 `/scratch/xiaobo/418326/xbt-8058088.46/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)N2CC[C@@H]([N@]3CC[C@H](NC(=O)OC(C)(C)C)CC3)C2)ccc1O) `ZINC001184252152.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184252152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184252152 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@@H]([N@]3CC[C@H](NC(=O)OC(C)(C)C)CC3)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.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 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, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 5, 5, 3, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 4, 6, 6, 6, 6, 6, 15, 24, 24, 26, 26, 26, 26, 6, 6, 3, 5, 5, 5, 5, 9, 9, 9, 5, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 15, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 6, 6, 6, 3, 3, 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, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 147) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/147 `/scratch/xiaobo/418326/xbt-8058088.46/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)N2CC[C@@H]([N@]3CC[C@@H](NC(=O)OC(C)(C)C)CC3)C2)ccc1O) `ZINC001184252152.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184252152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184252152 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@@H]([N@]3CC[C@@H](NC(=O)OC(C)(C)C)CC3)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.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 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, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [7, 5, 5, 5, 3, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 8, 8, 8, 8, 8, 16, 26, 26, 27, 27, 27, 27, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 5, 3, 3, 5, 5, 5, 5, 8, 8, 8, 8, 16, 27, 27, 27, 27, 27, 27, 27, 27, 27, 8, 8, 8, 8, 5, 5, 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, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 148) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/148 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/148' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@@H]([N@]3CC[C@H](NC(=O)OC(C)(C)C)CC3)C2)ccc1O) `ZINC001184252152.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184252152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184252152 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@@H]([N@]3CC[C@H](NC(=O)OC(C)(C)C)CC3)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.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 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, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 13, 23, 23, 23, 23, 23, 23, 5, 5, 3, 5, 5, 5, 5, 8, 8, 8, 5, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 5, 5, 5, 5, 3, 3, 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, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 149) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/149 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/149' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@@H]([N@]3CC[C@@H](NC(=O)OC(C)(C)C)CC3)C2)ccc1O) `ZINC001184252152.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184252152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184252152 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@@H]([N@]3CC[C@@H](NC(=O)OC(C)(C)C)CC3)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.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 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, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 13, 21, 21, 21, 21, 21, 21, 5, 5, 3, 6, 6, 6, 6, 9, 9, 9, 6, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 13, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 5, 5, 5, 3, 3, 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, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184252152 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152 Building ZINC001184252152 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184252152 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 146) grep: /scratch/xiaobo/418326/xbt-8058088.46/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)N2CC[C@@H]([N@]3CC[C@H](NC(=O)OC(C)(C)C)CC3)C2)ccc1O) `ZINC001184252152.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184252152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184252152 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@@H]([N@]3CC[C@H](NC(=O)OC(C)(C)C)CC3)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.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 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, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 5, 5, 3, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 4, 6, 6, 6, 6, 6, 15, 24, 24, 26, 26, 26, 26, 6, 6, 3, 5, 5, 5, 5, 9, 9, 9, 5, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 15, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 6, 6, 6, 3, 3, 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, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 147) grep: /scratch/xiaobo/418326/xbt-8058088.46/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)N2CC[C@@H]([N@]3CC[C@@H](NC(=O)OC(C)(C)C)CC3)C2)ccc1O) `ZINC001184252152.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184252152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184252152 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@@H]([N@]3CC[C@@H](NC(=O)OC(C)(C)C)CC3)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.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 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, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [7, 5, 5, 5, 3, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 8, 8, 8, 8, 8, 16, 26, 26, 27, 27, 27, 27, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 5, 3, 3, 5, 5, 5, 5, 8, 8, 8, 8, 16, 27, 27, 27, 27, 27, 27, 27, 27, 27, 8, 8, 8, 8, 5, 5, 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, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 148) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/148: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CC[C@@H]([N@]3CC[C@H](NC(=O)OC(C)(C)C)CC3)C2)ccc1O) `ZINC001184252152.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184252152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184252152 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@@H]([N@]3CC[C@H](NC(=O)OC(C)(C)C)CC3)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.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 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, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 13, 23, 23, 23, 23, 23, 23, 5, 5, 3, 5, 5, 5, 5, 8, 8, 8, 5, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 5, 5, 5, 5, 3, 3, 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, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 149) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/149: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CC[C@@H]([N@]3CC[C@@H](NC(=O)OC(C)(C)C)CC3)C2)ccc1O) `ZINC001184252152.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184252152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184252152 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@@H]([N@]3CC[C@@H](NC(=O)OC(C)(C)C)CC3)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.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 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, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 13, 21, 21, 21, 21, 21, 21, 5, 5, 3, 6, 6, 6, 6, 9, 9, 9, 6, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 13, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 5, 5, 5, 3, 3, 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, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184252152 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152 Building ZINC001184252152 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184252152 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 146) grep: /scratch/xiaobo/418326/xbt-8058088.46/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)N2CC[C@@H]([N@]3CC[C@H](NC(=O)OC(C)(C)C)CC3)C2)ccc1O) `ZINC001184252152.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184252152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184252152 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@@H]([N@]3CC[C@H](NC(=O)OC(C)(C)C)CC3)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.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 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, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 5, 5, 3, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 4, 6, 6, 6, 6, 6, 15, 24, 24, 26, 26, 26, 26, 6, 6, 3, 5, 5, 5, 5, 9, 9, 9, 5, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 15, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 6, 6, 6, 3, 3, 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, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 147) grep: /scratch/xiaobo/418326/xbt-8058088.46/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)N2CC[C@@H]([N@]3CC[C@@H](NC(=O)OC(C)(C)C)CC3)C2)ccc1O) `ZINC001184252152.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184252152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184252152 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@@H]([N@]3CC[C@@H](NC(=O)OC(C)(C)C)CC3)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.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 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, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [7, 5, 5, 5, 3, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 8, 8, 8, 8, 8, 16, 26, 26, 27, 27, 27, 27, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 5, 3, 3, 5, 5, 5, 5, 8, 8, 8, 8, 16, 27, 27, 27, 27, 27, 27, 27, 27, 27, 8, 8, 8, 8, 5, 5, 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, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 148) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/148: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CC[C@@H]([N@]3CC[C@H](NC(=O)OC(C)(C)C)CC3)C2)ccc1O) `ZINC001184252152.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184252152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184252152 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@@H]([N@]3CC[C@H](NC(=O)OC(C)(C)C)CC3)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.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 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, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 13, 23, 23, 23, 23, 23, 23, 5, 5, 3, 5, 5, 5, 5, 8, 8, 8, 5, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 5, 5, 5, 5, 3, 3, 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, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 149) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/149: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CC[C@@H]([N@]3CC[C@@H](NC(=O)OC(C)(C)C)CC3)C2)ccc1O) `ZINC001184252152.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184252152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184252152 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@@H]([N@]3CC[C@@H](NC(=O)OC(C)(C)C)CC3)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.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 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, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 13, 21, 21, 21, 21, 21, 21, 5, 5, 3, 6, 6, 6, 6, 9, 9, 9, 6, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 13, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 5, 5, 5, 3, 3, 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, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184252152 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152 Building ZINC001184252152 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184252152 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 146) grep: /scratch/xiaobo/418326/xbt-8058088.46/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)N2CC[C@@H]([N@]3CC[C@H](NC(=O)OC(C)(C)C)CC3)C2)ccc1O) `ZINC001184252152.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184252152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184252152 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@@H]([N@]3CC[C@H](NC(=O)OC(C)(C)C)CC3)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.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 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, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 5, 5, 3, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 4, 6, 6, 6, 6, 6, 15, 24, 24, 26, 26, 26, 26, 6, 6, 3, 5, 5, 5, 5, 9, 9, 9, 5, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 15, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 6, 6, 6, 3, 3, 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, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 147) grep: /scratch/xiaobo/418326/xbt-8058088.46/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)N2CC[C@@H]([N@]3CC[C@@H](NC(=O)OC(C)(C)C)CC3)C2)ccc1O) `ZINC001184252152.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184252152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184252152 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@@H]([N@]3CC[C@@H](NC(=O)OC(C)(C)C)CC3)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.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 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, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [7, 5, 5, 5, 3, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 8, 8, 8, 8, 8, 16, 26, 26, 27, 27, 27, 27, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 5, 3, 3, 5, 5, 5, 5, 8, 8, 8, 8, 16, 27, 27, 27, 27, 27, 27, 27, 27, 27, 8, 8, 8, 8, 5, 5, 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, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 148) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/148: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CC[C@@H]([N@]3CC[C@H](NC(=O)OC(C)(C)C)CC3)C2)ccc1O) `ZINC001184252152.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184252152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184252152 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@@H]([N@]3CC[C@H](NC(=O)OC(C)(C)C)CC3)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.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 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, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 13, 23, 23, 23, 23, 23, 23, 5, 5, 3, 5, 5, 5, 5, 8, 8, 8, 5, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 5, 5, 5, 5, 3, 3, 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, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 149) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/149: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CC[C@@H]([N@]3CC[C@@H](NC(=O)OC(C)(C)C)CC3)C2)ccc1O) `ZINC001184252152.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184252152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184252152 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@@H]([N@]3CC[C@@H](NC(=O)OC(C)(C)C)CC3)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.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 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, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 13, 21, 21, 21, 21, 21, 21, 5, 5, 3, 6, 6, 6, 6, 9, 9, 9, 6, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 13, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 5, 5, 5, 3, 3, 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, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184252152 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252152 Building ZINC001184252154 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184252154 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 150) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/150 `/scratch/xiaobo/418326/xbt-8058088.46/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)N2CC[C@H]([N@]3CC[C@H](NC(=O)OC(C)(C)C)CC3)C2)ccc1O) `ZINC001184252154.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184252154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184252154 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@H]([N@]3CC[C@H](NC(=O)OC(C)(C)C)CC3)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.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 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, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [7, 5, 5, 5, 3, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 13, 23, 23, 23, 23, 23, 23, 5, 5, 3, 5, 5, 5, 5, 7, 7, 7, 5, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 5, 5, 5, 5, 3, 3, 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, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 151) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/151 `/scratch/xiaobo/418326/xbt-8058088.46/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)N2CC[C@H]([N@]3CC[C@@H](NC(=O)OC(C)(C)C)CC3)C2)ccc1O) `ZINC001184252154.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184252154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184252154 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@H]([N@]3CC[C@@H](NC(=O)OC(C)(C)C)CC3)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.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 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, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [7, 5, 5, 5, 3, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 13, 23, 23, 23, 23, 23, 23, 5, 5, 3, 5, 5, 5, 5, 7, 7, 7, 5, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 5, 5, 5, 5, 3, 3, 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, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 152) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/152 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/152' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@H]([N@]3CC[C@H](NC(=O)OC(C)(C)C)CC3)C2)ccc1O) `ZINC001184252154.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184252154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184252154 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@H]([N@]3CC[C@H](NC(=O)OC(C)(C)C)CC3)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.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 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, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 4, 4, 4, 2, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 12, 22, 22, 22, 22, 22, 22, 6, 6, 3, 4, 4, 4, 4, 6, 6, 6, 4, 2, 2, 3, 3, 3, 3, 6, 6, 6, 6, 12, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 6, 3, 3, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 153) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/153 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/153' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@H]([N@]3CC[C@@H](NC(=O)OC(C)(C)C)CC3)C2)ccc1O) `ZINC001184252154.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184252154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184252154 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@H]([N@]3CC[C@@H](NC(=O)OC(C)(C)C)CC3)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.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 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, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 3, 5, 5, 5, 5, 5, 12, 21, 21, 23, 23, 23, 23, 5, 5, 2, 4, 4, 4, 4, 8, 8, 8, 4, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 12, 23, 23, 23, 23, 23, 23, 23, 23, 23, 5, 5, 5, 5, 2, 2, 4, 4, 8] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184252154 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154 Building ZINC001184252154 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184252154 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 150) grep: /scratch/xiaobo/418326/xbt-8058088.46/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)N2CC[C@H]([N@]3CC[C@H](NC(=O)OC(C)(C)C)CC3)C2)ccc1O) `ZINC001184252154.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184252154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184252154 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@H]([N@]3CC[C@H](NC(=O)OC(C)(C)C)CC3)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.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 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, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [7, 5, 5, 5, 3, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 13, 23, 23, 23, 23, 23, 23, 5, 5, 3, 5, 5, 5, 5, 7, 7, 7, 5, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 5, 5, 5, 5, 3, 3, 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, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 151) grep: /scratch/xiaobo/418326/xbt-8058088.46/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)N2CC[C@H]([N@]3CC[C@@H](NC(=O)OC(C)(C)C)CC3)C2)ccc1O) `ZINC001184252154.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184252154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184252154 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@H]([N@]3CC[C@@H](NC(=O)OC(C)(C)C)CC3)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.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 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, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [7, 5, 5, 5, 3, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 13, 23, 23, 23, 23, 23, 23, 5, 5, 3, 5, 5, 5, 5, 7, 7, 7, 5, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 5, 5, 5, 5, 3, 3, 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, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 152) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/152: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CC[C@H]([N@]3CC[C@H](NC(=O)OC(C)(C)C)CC3)C2)ccc1O) `ZINC001184252154.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184252154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184252154 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@H]([N@]3CC[C@H](NC(=O)OC(C)(C)C)CC3)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.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 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, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 4, 4, 4, 2, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 12, 22, 22, 22, 22, 22, 22, 6, 6, 3, 4, 4, 4, 4, 6, 6, 6, 4, 2, 2, 3, 3, 3, 3, 6, 6, 6, 6, 12, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 6, 3, 3, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 153) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/153: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CC[C@H]([N@]3CC[C@@H](NC(=O)OC(C)(C)C)CC3)C2)ccc1O) `ZINC001184252154.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184252154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184252154 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@H]([N@]3CC[C@@H](NC(=O)OC(C)(C)C)CC3)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.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 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, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 3, 5, 5, 5, 5, 5, 12, 21, 21, 23, 23, 23, 23, 5, 5, 2, 4, 4, 4, 4, 8, 8, 8, 4, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 12, 23, 23, 23, 23, 23, 23, 23, 23, 23, 5, 5, 5, 5, 2, 2, 4, 4, 8] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184252154 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154 Building ZINC001184252154 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184252154 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 150) grep: /scratch/xiaobo/418326/xbt-8058088.46/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)N2CC[C@H]([N@]3CC[C@H](NC(=O)OC(C)(C)C)CC3)C2)ccc1O) `ZINC001184252154.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184252154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184252154 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@H]([N@]3CC[C@H](NC(=O)OC(C)(C)C)CC3)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.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 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, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [7, 5, 5, 5, 3, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 13, 23, 23, 23, 23, 23, 23, 5, 5, 3, 5, 5, 5, 5, 7, 7, 7, 5, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 5, 5, 5, 5, 3, 3, 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, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 151) grep: /scratch/xiaobo/418326/xbt-8058088.46/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)N2CC[C@H]([N@]3CC[C@@H](NC(=O)OC(C)(C)C)CC3)C2)ccc1O) `ZINC001184252154.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184252154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184252154 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@H]([N@]3CC[C@@H](NC(=O)OC(C)(C)C)CC3)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.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 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, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [7, 5, 5, 5, 3, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 13, 23, 23, 23, 23, 23, 23, 5, 5, 3, 5, 5, 5, 5, 7, 7, 7, 5, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 5, 5, 5, 5, 3, 3, 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, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 152) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/152: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CC[C@H]([N@]3CC[C@H](NC(=O)OC(C)(C)C)CC3)C2)ccc1O) `ZINC001184252154.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184252154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184252154 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@H]([N@]3CC[C@H](NC(=O)OC(C)(C)C)CC3)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.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 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, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 4, 4, 4, 2, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 12, 22, 22, 22, 22, 22, 22, 6, 6, 3, 4, 4, 4, 4, 6, 6, 6, 4, 2, 2, 3, 3, 3, 3, 6, 6, 6, 6, 12, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 6, 3, 3, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 153) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/153: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CC[C@H]([N@]3CC[C@@H](NC(=O)OC(C)(C)C)CC3)C2)ccc1O) `ZINC001184252154.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184252154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184252154 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@H]([N@]3CC[C@@H](NC(=O)OC(C)(C)C)CC3)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.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 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, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 3, 5, 5, 5, 5, 5, 12, 21, 21, 23, 23, 23, 23, 5, 5, 2, 4, 4, 4, 4, 8, 8, 8, 4, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 12, 23, 23, 23, 23, 23, 23, 23, 23, 23, 5, 5, 5, 5, 2, 2, 4, 4, 8] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184252154 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154 Building ZINC001184252154 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184252154 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 150) grep: /scratch/xiaobo/418326/xbt-8058088.46/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)N2CC[C@H]([N@]3CC[C@H](NC(=O)OC(C)(C)C)CC3)C2)ccc1O) `ZINC001184252154.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184252154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184252154 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@H]([N@]3CC[C@H](NC(=O)OC(C)(C)C)CC3)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.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 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, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [7, 5, 5, 5, 3, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 13, 23, 23, 23, 23, 23, 23, 5, 5, 3, 5, 5, 5, 5, 7, 7, 7, 5, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 5, 5, 5, 5, 3, 3, 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, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 151) grep: /scratch/xiaobo/418326/xbt-8058088.46/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)N2CC[C@H]([N@]3CC[C@@H](NC(=O)OC(C)(C)C)CC3)C2)ccc1O) `ZINC001184252154.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184252154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184252154 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CC[C@H]([N@]3CC[C@@H](NC(=O)OC(C)(C)C)CC3)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.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 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, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [7, 5, 5, 5, 3, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 13, 23, 23, 23, 23, 23, 23, 5, 5, 3, 5, 5, 5, 5, 7, 7, 7, 5, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 5, 5, 5, 5, 3, 3, 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, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 152) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/152: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CC[C@H]([N@]3CC[C@H](NC(=O)OC(C)(C)C)CC3)C2)ccc1O) `ZINC001184252154.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184252154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184252154 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@H]([N@]3CC[C@H](NC(=O)OC(C)(C)C)CC3)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.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 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, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 4, 4, 4, 2, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 12, 22, 22, 22, 22, 22, 22, 6, 6, 3, 4, 4, 4, 4, 6, 6, 6, 4, 2, 2, 3, 3, 3, 3, 6, 6, 6, 6, 12, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 6, 3, 3, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 153) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/153: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CC[C@H]([N@]3CC[C@@H](NC(=O)OC(C)(C)C)CC3)C2)ccc1O) `ZINC001184252154.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184252154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184252154 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CC[C@H]([N@]3CC[C@@H](NC(=O)OC(C)(C)C)CC3)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.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 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, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 3, 5, 5, 5, 5, 5, 12, 21, 21, 23, 23, 23, 23, 5, 5, 2, 4, 4, 4, 4, 8, 8, 8, 4, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 12, 23, 23, 23, 23, 23, 23, 23, 23, 23, 5, 5, 5, 5, 2, 2, 4, 4, 8] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184252154 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252154 Building ZINC001184252157 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252157' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252157 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184252157 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252157/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252157 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 154) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/154 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/154' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)N(CCN(C)C)[C@@H]2CCCN(C(=O)OC(C)(C)C)C2)ccc1O) `ZINC001184252157.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184252157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 73 natoms 72 natoms 71 natoms 70 names: ZINC001184252157 none COc1cc(C[C@]([O-])([SiH3])C(=O)N(CCN(C)C)[C@@H]2CCCN(C(=O)OC(C)(C)C)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.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 6, 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, 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, 6, 1, 1, 1, 1, 2, 2, 4, 6, 6, 10, 10, 4, 4, 4, 4, 4, 4, 4, 6, 6, 10, 10, 10, 10, 4, 12, 12, 12, 12, 20, 20, 20, 12, 6, 6, 6, 6, 6, 6, 10, 10, 10, 10, 10, 10, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 12, 12, 24] 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, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 126 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252157 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252157/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252157 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 155) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/155 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/155' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N(CCN(C)C)[C@@H]2CCCN(C(=O)OC(C)(C)C)C2)ccc1O) `ZINC001184252157.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184252157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252157/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 73 natoms 72 natoms 71 natoms 70 names: ZINC001184252157 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N(CCN(C)C)[C@@H]2CCCN(C(=O)OC(C)(C)C)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.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 6, 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, 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: [22, 12, 12, 12, 6, 1, 1, 1, 1, 2, 2, 3, 5, 5, 8, 8, 3, 4, 4, 4, 4, 4, 4, 8, 8, 12, 12, 12, 12, 4, 12, 12, 12, 12, 22, 22, 22, 12, 6, 6, 5, 5, 5, 5, 8, 8, 8, 8, 8, 8, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 12, 12, 24] 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, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 129 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252157 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184252157 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252157/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252157/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252157 Building ZINC001184252157 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252157' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252157 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184252157 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252157/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252157 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 154) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N(CCN(C)C)[C@@H]2CCCN(C(=O)OC(C)(C)C)C2)ccc1O) `ZINC001184252157.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184252157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 73 natoms 72 natoms 71 natoms 70 names: ZINC001184252157 none COc1cc(C[C@]([O-])([SiH3])C(=O)N(CCN(C)C)[C@@H]2CCCN(C(=O)OC(C)(C)C)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.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 6, 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, 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, 6, 1, 1, 1, 1, 2, 2, 4, 6, 6, 10, 10, 4, 4, 4, 4, 4, 4, 4, 6, 6, 10, 10, 10, 10, 4, 12, 12, 12, 12, 20, 20, 20, 12, 6, 6, 6, 6, 6, 6, 10, 10, 10, 10, 10, 10, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 12, 12, 24] 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, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 126 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252157 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252157/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252157 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 155) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)N(CCN(C)C)[C@@H]2CCCN(C(=O)OC(C)(C)C)C2)ccc1O) `ZINC001184252157.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184252157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252157/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 73 natoms 72 natoms 71 natoms 70 names: ZINC001184252157 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N(CCN(C)C)[C@@H]2CCCN(C(=O)OC(C)(C)C)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.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 6, 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, 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: [22, 12, 12, 12, 6, 1, 1, 1, 1, 2, 2, 3, 5, 5, 8, 8, 3, 4, 4, 4, 4, 4, 4, 8, 8, 12, 12, 12, 12, 4, 12, 12, 12, 12, 22, 22, 22, 12, 6, 6, 5, 5, 5, 5, 8, 8, 8, 8, 8, 8, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 12, 12, 24] 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, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 129 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252157 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184252157 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252157/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252157/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252157 Building ZINC001184252159 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252159' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252159 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184252159 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252159/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252159 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 156) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/156 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/156' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)N(CCN(C)C)[C@H]2CCCN(C(=O)OC(C)(C)C)C2)ccc1O) `ZINC001184252159.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184252159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 73 natoms 72 natoms 71 natoms 70 names: ZINC001184252159 none COc1cc(C[C@]([O-])([SiH3])C(=O)N(CCN(C)C)[C@H]2CCCN(C(=O)OC(C)(C)C)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.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 6, 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, 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, 7, 7, 7, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 4, 2, 3, 3, 3, 3, 3, 3, 13, 13, 19, 21, 21, 21, 3, 7, 7, 7, 7, 11, 11, 11, 7, 4, 4, 2, 2, 2, 2, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 3, 3, 7, 7, 14] 100 rigid atoms, others: [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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 106 number of broken/clashed sets: 92 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252159 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252159/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252159 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 157) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/157 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/157' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N(CCN(C)C)[C@H]2CCCN(C(=O)OC(C)(C)C)C2)ccc1O) `ZINC001184252159.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184252159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252159/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 73 natoms 72 natoms 71 natoms 70 names: ZINC001184252159 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N(CCN(C)C)[C@H]2CCCN(C(=O)OC(C)(C)C)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.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 6, 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, 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, 8, 8, 8, 5, 1, 1, 1, 1, 2, 2, 2, 3, 3, 4, 4, 3, 4, 4, 4, 4, 4, 4, 16, 16, 28, 31, 31, 31, 4, 8, 8, 8, 8, 11, 11, 11, 8, 5, 5, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 31, 31, 31, 31, 31, 31, 31, 31, 31, 4, 4, 8, 8, 16] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 134 number of broken/clashed sets: 74 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252159 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184252159 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252159/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252159/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252159 Building ZINC001184252159 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252159' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252159 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184252159 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252159/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252159 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 156) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N(CCN(C)C)[C@H]2CCCN(C(=O)OC(C)(C)C)C2)ccc1O) `ZINC001184252159.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184252159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 73 natoms 72 natoms 71 natoms 70 names: ZINC001184252159 none COc1cc(C[C@]([O-])([SiH3])C(=O)N(CCN(C)C)[C@H]2CCCN(C(=O)OC(C)(C)C)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.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 6, 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, 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, 7, 7, 7, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 4, 2, 3, 3, 3, 3, 3, 3, 13, 13, 19, 21, 21, 21, 3, 7, 7, 7, 7, 11, 11, 11, 7, 4, 4, 2, 2, 2, 2, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 3, 3, 7, 7, 14] 100 rigid atoms, others: [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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 106 number of broken/clashed sets: 92 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252159 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252159/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252159 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 157) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)N(CCN(C)C)[C@H]2CCCN(C(=O)OC(C)(C)C)C2)ccc1O) `ZINC001184252159.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184252159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252159/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 73 natoms 72 natoms 71 natoms 70 names: ZINC001184252159 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N(CCN(C)C)[C@H]2CCCN(C(=O)OC(C)(C)C)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.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 6, 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, 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, 8, 8, 8, 5, 1, 1, 1, 1, 2, 2, 2, 3, 3, 4, 4, 3, 4, 4, 4, 4, 4, 4, 16, 16, 28, 31, 31, 31, 4, 8, 8, 8, 8, 11, 11, 11, 8, 5, 5, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 31, 31, 31, 31, 31, 31, 31, 31, 31, 4, 4, 8, 8, 16] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 134 number of broken/clashed sets: 74 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252159 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184252159 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252159/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252159/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252159 Building ZINC001184252287 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184252287 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 158) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/158 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/158' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCCN(c3cc(Cl)nc(SC)n3)CC2)ccc1O) `ZINC001184252287.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184252287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184252287 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCCN(c3cc(Cl)nc(SC)n3)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.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'S.3', 'C.3', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 16, 8, 1, 14, 5, 8, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [10, 9, 9, 9, 5, 1, 1, 1, 1, 7, 8, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 17, 27, 17, 8, 8, 9, 9, 9, 9, 10, 10, 10, 9, 5, 5, 8, 8, 8, 8, 8, 8, 17, 27, 27, 27, 8, 8, 8, 8, 9, 9, 18] 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]) total number of confs: 89 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 159) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/159 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/159' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCCN(c3cc(Cl)nc(SC)n3)CC2)ccc1O) `ZINC001184252287.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184252287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184252287 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCCN(c3cc(Cl)nc(SC)n3)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.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'S.3', 'C.3', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 16, 8, 1, 14, 5, 8, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [11, 10, 10, 10, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 16, 16, 16, 16, 16, 16, 25, 16, 7, 7, 10, 10, 10, 10, 11, 11, 11, 10, 5, 5, 7, 7, 7, 7, 7, 7, 16, 25, 25, 25, 7, 7, 7, 7, 10, 10, 20] 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]) total number of confs: 92 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 160) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/160 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/160' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCCN(c3cc(Cl)nc(SC)n3)CC2)ccc1O) `ZINC001184252287.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184252287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184252287 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCCN(c3cc(Cl)nc(SC)n3)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.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'S.3', 'C.3', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 16, 8, 1, 14, 5, 8, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [10, 9, 9, 9, 5, 1, 1, 1, 1, 7, 8, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 17, 27, 17, 8, 8, 9, 9, 9, 9, 10, 10, 10, 9, 5, 5, 8, 8, 8, 8, 8, 8, 17, 27, 27, 27, 8, 8, 8, 8, 9, 9, 18] 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]) total number of confs: 89 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 161) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/161 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/161' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCCN(c3cc(Cl)nc(SC)n3)CC2)ccc1O) `ZINC001184252287.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184252287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184252287 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCCN(c3cc(Cl)nc(SC)n3)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.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'S.3', 'C.3', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 16, 8, 1, 14, 5, 8, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [11, 10, 10, 10, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 16, 16, 16, 16, 16, 16, 25, 16, 7, 7, 10, 10, 10, 10, 11, 11, 11, 10, 5, 5, 7, 7, 7, 7, 7, 7, 16, 25, 25, 25, 7, 7, 7, 7, 10, 10, 20] 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]) total number of confs: 92 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184252287 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287 Building ZINC001184252287 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184252287 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 158) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCCN(c3cc(Cl)nc(SC)n3)CC2)ccc1O) `ZINC001184252287.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184252287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184252287 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCCN(c3cc(Cl)nc(SC)n3)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.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'S.3', 'C.3', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 16, 8, 1, 14, 5, 8, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [10, 9, 9, 9, 5, 1, 1, 1, 1, 7, 8, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 17, 27, 17, 8, 8, 9, 9, 9, 9, 10, 10, 10, 9, 5, 5, 8, 8, 8, 8, 8, 8, 17, 27, 27, 27, 8, 8, 8, 8, 9, 9, 18] 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]) total number of confs: 89 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 159) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCCN(c3cc(Cl)nc(SC)n3)CC2)ccc1O) `ZINC001184252287.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184252287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184252287 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCCN(c3cc(Cl)nc(SC)n3)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.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'S.3', 'C.3', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 16, 8, 1, 14, 5, 8, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [11, 10, 10, 10, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 16, 16, 16, 16, 16, 16, 25, 16, 7, 7, 10, 10, 10, 10, 11, 11, 11, 10, 5, 5, 7, 7, 7, 7, 7, 7, 16, 25, 25, 25, 7, 7, 7, 7, 10, 10, 20] 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]) total number of confs: 92 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 160) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/160: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCCN(c3cc(Cl)nc(SC)n3)CC2)ccc1O) `ZINC001184252287.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184252287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184252287 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCCN(c3cc(Cl)nc(SC)n3)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.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'S.3', 'C.3', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 16, 8, 1, 14, 5, 8, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [10, 9, 9, 9, 5, 1, 1, 1, 1, 7, 8, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 17, 27, 17, 8, 8, 9, 9, 9, 9, 10, 10, 10, 9, 5, 5, 8, 8, 8, 8, 8, 8, 17, 27, 27, 27, 8, 8, 8, 8, 9, 9, 18] 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]) total number of confs: 89 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 161) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/161: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCCN(c3cc(Cl)nc(SC)n3)CC2)ccc1O) `ZINC001184252287.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184252287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184252287 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCCN(c3cc(Cl)nc(SC)n3)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.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'S.3', 'C.3', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 16, 8, 1, 14, 5, 8, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [11, 10, 10, 10, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 16, 16, 16, 16, 16, 16, 25, 16, 7, 7, 10, 10, 10, 10, 11, 11, 11, 10, 5, 5, 7, 7, 7, 7, 7, 7, 16, 25, 25, 25, 7, 7, 7, 7, 10, 10, 20] 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]) total number of confs: 92 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184252287 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287 Building ZINC001184252287 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184252287 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 158) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCCN(c3cc(Cl)nc(SC)n3)CC2)ccc1O) `ZINC001184252287.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184252287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184252287 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCCN(c3cc(Cl)nc(SC)n3)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.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'S.3', 'C.3', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 16, 8, 1, 14, 5, 8, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [10, 9, 9, 9, 5, 1, 1, 1, 1, 7, 8, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 17, 27, 17, 8, 8, 9, 9, 9, 9, 10, 10, 10, 9, 5, 5, 8, 8, 8, 8, 8, 8, 17, 27, 27, 27, 8, 8, 8, 8, 9, 9, 18] 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]) total number of confs: 89 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 159) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCCN(c3cc(Cl)nc(SC)n3)CC2)ccc1O) `ZINC001184252287.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184252287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184252287 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCCN(c3cc(Cl)nc(SC)n3)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.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'S.3', 'C.3', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 16, 8, 1, 14, 5, 8, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [11, 10, 10, 10, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 16, 16, 16, 16, 16, 16, 25, 16, 7, 7, 10, 10, 10, 10, 11, 11, 11, 10, 5, 5, 7, 7, 7, 7, 7, 7, 16, 25, 25, 25, 7, 7, 7, 7, 10, 10, 20] 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]) total number of confs: 92 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 160) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/160: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCCN(c3cc(Cl)nc(SC)n3)CC2)ccc1O) `ZINC001184252287.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184252287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184252287 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCCN(c3cc(Cl)nc(SC)n3)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.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'S.3', 'C.3', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 16, 8, 1, 14, 5, 8, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [10, 9, 9, 9, 5, 1, 1, 1, 1, 7, 8, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 17, 27, 17, 8, 8, 9, 9, 9, 9, 10, 10, 10, 9, 5, 5, 8, 8, 8, 8, 8, 8, 17, 27, 27, 27, 8, 8, 8, 8, 9, 9, 18] 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]) total number of confs: 89 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 161) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/161: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCCN(c3cc(Cl)nc(SC)n3)CC2)ccc1O) `ZINC001184252287.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184252287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184252287 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCCN(c3cc(Cl)nc(SC)n3)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.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'S.3', 'C.3', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 16, 8, 1, 14, 5, 8, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [11, 10, 10, 10, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 16, 16, 16, 16, 16, 16, 25, 16, 7, 7, 10, 10, 10, 10, 11, 11, 11, 10, 5, 5, 7, 7, 7, 7, 7, 7, 16, 25, 25, 25, 7, 7, 7, 7, 10, 10, 20] 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]) total number of confs: 92 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184252287 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287 Building ZINC001184252287 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184252287 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 158) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCCN(c3cc(Cl)nc(SC)n3)CC2)ccc1O) `ZINC001184252287.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184252287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184252287 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCCN(c3cc(Cl)nc(SC)n3)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.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'S.3', 'C.3', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 16, 8, 1, 14, 5, 8, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [10, 9, 9, 9, 5, 1, 1, 1, 1, 7, 8, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 17, 27, 17, 8, 8, 9, 9, 9, 9, 10, 10, 10, 9, 5, 5, 8, 8, 8, 8, 8, 8, 17, 27, 27, 27, 8, 8, 8, 8, 9, 9, 18] 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]) total number of confs: 89 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 159) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCCN(c3cc(Cl)nc(SC)n3)CC2)ccc1O) `ZINC001184252287.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184252287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184252287 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCCN(c3cc(Cl)nc(SC)n3)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.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'S.3', 'C.3', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 16, 8, 1, 14, 5, 8, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [11, 10, 10, 10, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 16, 16, 16, 16, 16, 16, 25, 16, 7, 7, 10, 10, 10, 10, 11, 11, 11, 10, 5, 5, 7, 7, 7, 7, 7, 7, 16, 25, 25, 25, 7, 7, 7, 7, 10, 10, 20] 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]) total number of confs: 92 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 160) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/160: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCCN(c3cc(Cl)nc(SC)n3)CC2)ccc1O) `ZINC001184252287.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184252287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184252287 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCCN(c3cc(Cl)nc(SC)n3)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.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'S.3', 'C.3', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 16, 8, 1, 14, 5, 8, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [10, 9, 9, 9, 5, 1, 1, 1, 1, 7, 8, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 17, 27, 17, 8, 8, 9, 9, 9, 9, 10, 10, 10, 9, 5, 5, 8, 8, 8, 8, 8, 8, 17, 27, 27, 27, 8, 8, 8, 8, 9, 9, 18] 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]) total number of confs: 89 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 161) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/161: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCCN(c3cc(Cl)nc(SC)n3)CC2)ccc1O) `ZINC001184252287.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184252287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184252287 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCCN(c3cc(Cl)nc(SC)n3)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.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'S.3', 'C.3', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 16, 8, 1, 14, 5, 8, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [11, 10, 10, 10, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 16, 16, 16, 16, 16, 16, 25, 16, 7, 7, 10, 10, 10, 10, 11, 11, 11, 10, 5, 5, 7, 7, 7, 7, 7, 7, 16, 25, 25, 25, 7, 7, 7, 7, 10, 10, 20] 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]) total number of confs: 92 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184252287 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252287 Building ZINC001184252324 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252324' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252324 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184252324 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252324/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252324 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 162) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/162 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/162' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cn2nc([C@H]3CCCN(C(=O)[C@@]([O-])([SiH3])Cc4ccc(O)c(OC)c4)C3)sc2n1) `ZINC001184252324.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184252324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184252324 none CCOC(=O)c1cn2nc([C@H]3CCCN(C(=O)[C@@]([O-])([SiH3])Cc4ccc(O)c(OC)c4)C3)sc2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 14, 1, 8, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [30, 23, 23, 11, 23, 11, 11, 11, 11, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 5, 10, 10, 10, 10, 10, 10, 20, 10, 2, 11, 11, 11, 30, 30, 30, 30, 30, 11, 2, 2, 2, 2, 2, 2, 5, 5, 10, 10, 20, 20, 20, 20, 10, 2, 2] 100 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: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252324 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252324/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252324 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 163) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/163 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/163' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cn2nc([C@H]3CCCN(C(=O)[C@]([O-])([SiH3])Cc4ccc(O)c(OC)c4)C3)sc2n1) `ZINC001184252324.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184252324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252324/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184252324 none CCOC(=O)c1cn2nc([C@H]3CCCN(C(=O)[C@]([O-])([SiH3])Cc4ccc(O)c(OC)c4)C3)sc2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 14, 1, 8, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [28, 21, 21, 13, 21, 13, 13, 13, 13, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 4, 7, 7, 7, 7, 7, 7, 14, 7, 3, 13, 13, 13, 28, 28, 28, 28, 28, 13, 3, 3, 3, 3, 3, 3, 4, 4, 7, 7, 14, 14, 14, 14, 7, 3, 3] 100 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: 129 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252324 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184252324 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252324/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252324/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252324 Building ZINC001184252324 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252324' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252324 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184252324 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252324/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252324 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 162) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCOC(=O)c1cn2nc([C@H]3CCCN(C(=O)[C@@]([O-])([SiH3])Cc4ccc(O)c(OC)c4)C3)sc2n1) `ZINC001184252324.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184252324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184252324 none CCOC(=O)c1cn2nc([C@H]3CCCN(C(=O)[C@@]([O-])([SiH3])Cc4ccc(O)c(OC)c4)C3)sc2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 14, 1, 8, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [30, 23, 23, 11, 23, 11, 11, 11, 11, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 5, 10, 10, 10, 10, 10, 10, 20, 10, 2, 11, 11, 11, 30, 30, 30, 30, 30, 11, 2, 2, 2, 2, 2, 2, 5, 5, 10, 10, 20, 20, 20, 20, 10, 2, 2] 100 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: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252324 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252324/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252324 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 163) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCOC(=O)c1cn2nc([C@H]3CCCN(C(=O)[C@]([O-])([SiH3])Cc4ccc(O)c(OC)c4)C3)sc2n1) `ZINC001184252324.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184252324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252324/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184252324 none CCOC(=O)c1cn2nc([C@H]3CCCN(C(=O)[C@]([O-])([SiH3])Cc4ccc(O)c(OC)c4)C3)sc2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 14, 1, 8, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [28, 21, 21, 13, 21, 13, 13, 13, 13, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 4, 7, 7, 7, 7, 7, 7, 14, 7, 3, 13, 13, 13, 28, 28, 28, 28, 28, 13, 3, 3, 3, 3, 3, 3, 4, 4, 7, 7, 14, 14, 14, 14, 7, 3, 3] 100 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: 129 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252324 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184252324 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252324/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252324/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252324 Building ZINC001184252325 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252325' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252325 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184252325 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252325/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252325 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 164) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/164 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/164' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cn2nc([C@@H]3CCCN(C(=O)[C@@]([O-])([SiH3])Cc4ccc(O)c(OC)c4)C3)sc2n1) `ZINC001184252325.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184252325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184252325 none CCOC(=O)c1cn2nc([C@@H]3CCCN(C(=O)[C@@]([O-])([SiH3])Cc4ccc(O)c(OC)c4)C3)sc2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 14, 1, 8, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [28, 20, 19, 10, 19, 10, 10, 10, 10, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 4, 7, 7, 7, 7, 7, 7, 13, 7, 3, 10, 10, 10, 28, 28, 28, 28, 28, 10, 3, 3, 3, 3, 3, 3, 4, 4, 7, 7, 14, 13, 13, 13, 7, 3, 3] 100 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: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252325 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252325/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252325 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 165) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/165 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/165' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cn2nc([C@@H]3CCCN(C(=O)[C@]([O-])([SiH3])Cc4ccc(O)c(OC)c4)C3)sc2n1) `ZINC001184252325.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184252325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252325/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184252325 none CCOC(=O)c1cn2nc([C@@H]3CCCN(C(=O)[C@]([O-])([SiH3])Cc4ccc(O)c(OC)c4)C3)sc2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 14, 1, 8, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [33, 22, 22, 13, 22, 13, 13, 13, 13, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 16, 9, 2, 13, 13, 13, 33, 33, 33, 33, 33, 13, 2, 2, 2, 2, 2, 2, 5, 5, 9, 9, 18, 16, 16, 16, 9, 2, 2] 100 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: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252325 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184252325 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252325/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252325/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252325 Building ZINC001184252325 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252325' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252325 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184252325 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252325/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252325 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 164) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCOC(=O)c1cn2nc([C@@H]3CCCN(C(=O)[C@@]([O-])([SiH3])Cc4ccc(O)c(OC)c4)C3)sc2n1) `ZINC001184252325.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184252325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184252325 none CCOC(=O)c1cn2nc([C@@H]3CCCN(C(=O)[C@@]([O-])([SiH3])Cc4ccc(O)c(OC)c4)C3)sc2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 14, 1, 8, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [28, 20, 19, 10, 19, 10, 10, 10, 10, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 4, 7, 7, 7, 7, 7, 7, 13, 7, 3, 10, 10, 10, 28, 28, 28, 28, 28, 10, 3, 3, 3, 3, 3, 3, 4, 4, 7, 7, 14, 13, 13, 13, 7, 3, 3] 100 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: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252325 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252325/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252325 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 165) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCOC(=O)c1cn2nc([C@@H]3CCCN(C(=O)[C@]([O-])([SiH3])Cc4ccc(O)c(OC)c4)C3)sc2n1) `ZINC001184252325.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184252325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252325/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184252325 none CCOC(=O)c1cn2nc([C@@H]3CCCN(C(=O)[C@]([O-])([SiH3])Cc4ccc(O)c(OC)c4)C3)sc2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 14, 1, 8, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [33, 22, 22, 13, 22, 13, 13, 13, 13, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 16, 9, 2, 13, 13, 13, 33, 33, 33, 33, 33, 13, 2, 2, 2, 2, 2, 2, 5, 5, 9, 9, 18, 16, 16, 16, 9, 2, 2] 100 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: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252325 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184252325 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252325/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252325/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252325 Building ZINC001184252662 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252662' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252662 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184252662 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252662/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252662 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 166) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/166 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/166' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC(c3nc(c4ccc(S(C)(=O)=O)cc4)no3)CC2)ccc1O) `ZINC001184252662.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184252662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252662/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184252662 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC(c3nc(c4ccc(S(C)(=O)=O)cc4)no3)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.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 8, 12, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 3, 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] 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, 3, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 14, 14, 14, 20, 20, 18, 20, 32, 32, 32, 20, 20, 14, 14, 2, 2, 6, 6, 6, 6, 9, 9, 9, 6, 3, 3, 2, 2, 2, 2, 2, 20, 20, 32, 32, 32, 20, 20, 2, 2, 2, 2, 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, 55, 56, 57, 58, 59]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252662 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252662/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252662 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 167) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/167 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/167' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC(c3nc(c4ccc(S(C)(=O)=O)cc4)no3)CC2)ccc1O) `ZINC001184252662.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184252662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252662/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184252662 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC(c3nc(c4ccc(S(C)(=O)=O)cc4)no3)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.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 8, 12, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 3, 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] 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, 5, 5, 5, 3, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 17, 17, 17, 17, 17, 17, 17, 26, 26, 26, 17, 17, 17, 17, 2, 2, 5, 5, 5, 5, 7, 7, 7, 5, 3, 3, 2, 2, 2, 2, 2, 17, 17, 26, 26, 26, 17, 17, 2, 2, 2, 2, 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: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252662 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184252662 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252662/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252662/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252662 Building ZINC001184252662 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252662' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252662 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184252662 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252662/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252662 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 166) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC(c3nc(c4ccc(S(C)(=O)=O)cc4)no3)CC2)ccc1O) `ZINC001184252662.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184252662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252662/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184252662 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC(c3nc(c4ccc(S(C)(=O)=O)cc4)no3)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.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 8, 12, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 3, 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] 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, 3, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 14, 14, 14, 20, 20, 18, 20, 32, 32, 32, 20, 20, 14, 14, 2, 2, 6, 6, 6, 6, 9, 9, 9, 6, 3, 3, 2, 2, 2, 2, 2, 20, 20, 32, 32, 32, 20, 20, 2, 2, 2, 2, 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, 55, 56, 57, 58, 59]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252662 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252662/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252662 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 167) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC(c3nc(c4ccc(S(C)(=O)=O)cc4)no3)CC2)ccc1O) `ZINC001184252662.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184252662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252662/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184252662 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC(c3nc(c4ccc(S(C)(=O)=O)cc4)no3)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.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 8, 12, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 3, 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] 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, 5, 5, 5, 3, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 17, 17, 17, 17, 17, 17, 17, 26, 26, 26, 17, 17, 17, 17, 2, 2, 5, 5, 5, 5, 7, 7, 7, 5, 3, 3, 2, 2, 2, 2, 2, 17, 17, 26, 26, 26, 17, 17, 2, 2, 2, 2, 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: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252662 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184252662 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252662/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252662/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252662 Building ZINC001184252697 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252697' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252697 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184252697 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252697/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252697 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 168) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/168 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/168' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)N(c2onc(C)c2C)S(=O)(=O)c2ccc(N)cc2)ccc1O) `ZINC001184252697.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184252697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184252697 none COc1cc(C[C@]([O-])([SiH3])C(=O)N(c2onc(C)c2C)S(=O)(=O)c2ccc(N)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.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 12, 8, 1, 5, 1, 5, 14, 11, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 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] 1 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: [14, 6, 6, 6, 3, 1, 1, 1, 1, 2, 2, 3, 6, 6, 6, 6, 6, 6, 3, 4, 4, 4, 8, 8, 4, 6, 8, 8, 6, 6, 6, 6, 14, 14, 14, 6, 3, 3, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 8, 6, 6, 12] 44 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 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/418326/xbt-8058088.46/working/building/ZINC001184252697 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252697/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252697 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 169) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/169 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/169' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N(c2onc(C)c2C)S(=O)(=O)c2ccc(N)cc2)ccc1O) `ZINC001184252697.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184252697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252697/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184252697 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N(c2onc(C)c2C)S(=O)(=O)c2ccc(N)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.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 12, 8, 1, 5, 1, 5, 14, 11, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 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] 1 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 6, 6, 3, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 8, 8, 3, 6, 6, 6, 10, 10, 10, 10, 10, 10, 6, 6, 6, 6, 14, 14, 14, 6, 3, 3, 8, 8, 8, 8, 8, 8, 10, 10, 10, 10, 10, 10, 6, 6, 12] 56 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252697 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184252697 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252697/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252697/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252697 Building ZINC001184252697 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252697' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252697 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184252697 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252697/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252697 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 168) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N(c2onc(C)c2C)S(=O)(=O)c2ccc(N)cc2)ccc1O) `ZINC001184252697.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184252697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184252697 none COc1cc(C[C@]([O-])([SiH3])C(=O)N(c2onc(C)c2C)S(=O)(=O)c2ccc(N)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.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 12, 8, 1, 5, 1, 5, 14, 11, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 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] 1 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: [14, 6, 6, 6, 3, 1, 1, 1, 1, 2, 2, 3, 6, 6, 6, 6, 6, 6, 3, 4, 4, 4, 8, 8, 4, 6, 8, 8, 6, 6, 6, 6, 14, 14, 14, 6, 3, 3, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 8, 6, 6, 12] 44 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 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/418326/xbt-8058088.46/working/building/ZINC001184252697 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252697/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252697 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 169) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)N(c2onc(C)c2C)S(=O)(=O)c2ccc(N)cc2)ccc1O) `ZINC001184252697.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184252697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252697/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184252697 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N(c2onc(C)c2C)S(=O)(=O)c2ccc(N)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.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 12, 8, 1, 5, 1, 5, 14, 11, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 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] 1 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 6, 6, 3, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 8, 8, 3, 6, 6, 6, 10, 10, 10, 10, 10, 10, 6, 6, 6, 6, 14, 14, 14, 6, 3, 3, 8, 8, 8, 8, 8, 8, 10, 10, 10, 10, 10, 10, 6, 6, 12] 56 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252697 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184252697 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252697/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252697/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252697 Building ZINC001184252755 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184252755 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 170) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/170 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/170' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)N2Cc3cc(OC)c(OC)cc3C(=O)C23CCN(C)CC3)ccc1O) `ZINC001184252755.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184252755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184252755 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2Cc3cc(OC)c(OC)cc3C(=O)C23CCN(C)CC3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 11, 5, 5, 5, 10, 5, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 10, 10, 10, 5, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 17, 7, 7, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 10, 10, 10, 10, 17, 17, 17, 10, 5, 5, 7, 7, 7, 17, 17, 17, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 10, 10, 20] 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, 60, 61, 62, 63, 64]) total number of confs: 98 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 171) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/171 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/171' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)N2Cc3cc(OC)c(OC)cc3C(=O)C23CCN(C)CC3)ccc1O) `ZINC001184252755.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184252755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184252755 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2Cc3cc(OC)c(OC)cc3C(=O)C23CCN(C)CC3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 11, 5, 5, 5, 10, 5, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 10, 10, 10, 5, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 17, 7, 7, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 10, 10, 10, 10, 17, 17, 17, 10, 5, 5, 7, 7, 7, 17, 17, 17, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 10, 10, 20] 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, 60, 61, 62, 63, 64]) total number of confs: 98 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 172) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/172 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/172' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2Cc3cc(OC)c(OC)cc3C(=O)C23CCN(C)CC3)ccc1O) `ZINC001184252755.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184252755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184252755 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2Cc3cc(OC)c(OC)cc3C(=O)C23CCN(C)CC3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 11, 5, 5, 5, 10, 5, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [14, 10, 10, 10, 5, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 8, 20, 8, 8, 17, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 10, 10, 10, 10, 14, 14, 14, 10, 5, 5, 8, 8, 8, 20, 20, 20, 17, 17, 17, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 10, 10, 20] 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, 60, 61, 62, 63, 64]) total number of confs: 104 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 173) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/173 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/173' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2Cc3cc(OC)c(OC)cc3C(=O)C23CCN(C)CC3)ccc1O) `ZINC001184252755.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184252755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184252755 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2Cc3cc(OC)c(OC)cc3C(=O)C23CCN(C)CC3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 11, 5, 5, 5, 10, 5, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [14, 10, 10, 10, 5, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 8, 20, 8, 8, 17, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 10, 10, 10, 10, 14, 14, 14, 10, 5, 5, 8, 8, 8, 20, 20, 20, 17, 17, 17, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 10, 10, 20] 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, 60, 61, 62, 63, 64]) total number of confs: 104 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184252755 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755 Building ZINC001184252755 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184252755 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 170) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N2Cc3cc(OC)c(OC)cc3C(=O)C23CCN(C)CC3)ccc1O) `ZINC001184252755.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184252755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184252755 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2Cc3cc(OC)c(OC)cc3C(=O)C23CCN(C)CC3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 11, 5, 5, 5, 10, 5, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 10, 10, 10, 5, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 17, 7, 7, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 10, 10, 10, 10, 17, 17, 17, 10, 5, 5, 7, 7, 7, 17, 17, 17, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 10, 10, 20] 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, 60, 61, 62, 63, 64]) total number of confs: 98 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 171) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N2Cc3cc(OC)c(OC)cc3C(=O)C23CCN(C)CC3)ccc1O) `ZINC001184252755.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184252755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184252755 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2Cc3cc(OC)c(OC)cc3C(=O)C23CCN(C)CC3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 11, 5, 5, 5, 10, 5, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 10, 10, 10, 5, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 17, 7, 7, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 10, 10, 10, 10, 17, 17, 17, 10, 5, 5, 7, 7, 7, 17, 17, 17, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 10, 10, 20] 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, 60, 61, 62, 63, 64]) total number of confs: 98 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 172) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/172: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2Cc3cc(OC)c(OC)cc3C(=O)C23CCN(C)CC3)ccc1O) `ZINC001184252755.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184252755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184252755 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2Cc3cc(OC)c(OC)cc3C(=O)C23CCN(C)CC3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 11, 5, 5, 5, 10, 5, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [14, 10, 10, 10, 5, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 8, 20, 8, 8, 17, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 10, 10, 10, 10, 14, 14, 14, 10, 5, 5, 8, 8, 8, 20, 20, 20, 17, 17, 17, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 10, 10, 20] 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, 60, 61, 62, 63, 64]) total number of confs: 104 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 173) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/173: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2Cc3cc(OC)c(OC)cc3C(=O)C23CCN(C)CC3)ccc1O) `ZINC001184252755.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184252755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184252755 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2Cc3cc(OC)c(OC)cc3C(=O)C23CCN(C)CC3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 11, 5, 5, 5, 10, 5, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [14, 10, 10, 10, 5, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 8, 20, 8, 8, 17, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 10, 10, 10, 10, 14, 14, 14, 10, 5, 5, 8, 8, 8, 20, 20, 20, 17, 17, 17, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 10, 10, 20] 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, 60, 61, 62, 63, 64]) total number of confs: 104 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184252755 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755 Building ZINC001184252755 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184252755 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 170) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N2Cc3cc(OC)c(OC)cc3C(=O)C23CCN(C)CC3)ccc1O) `ZINC001184252755.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184252755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184252755 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2Cc3cc(OC)c(OC)cc3C(=O)C23CCN(C)CC3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 11, 5, 5, 5, 10, 5, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 10, 10, 10, 5, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 17, 7, 7, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 10, 10, 10, 10, 17, 17, 17, 10, 5, 5, 7, 7, 7, 17, 17, 17, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 10, 10, 20] 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, 60, 61, 62, 63, 64]) total number of confs: 98 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 171) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N2Cc3cc(OC)c(OC)cc3C(=O)C23CCN(C)CC3)ccc1O) `ZINC001184252755.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184252755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184252755 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2Cc3cc(OC)c(OC)cc3C(=O)C23CCN(C)CC3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 11, 5, 5, 5, 10, 5, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 10, 10, 10, 5, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 17, 7, 7, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 10, 10, 10, 10, 17, 17, 17, 10, 5, 5, 7, 7, 7, 17, 17, 17, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 10, 10, 20] 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, 60, 61, 62, 63, 64]) total number of confs: 98 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 172) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/172: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2Cc3cc(OC)c(OC)cc3C(=O)C23CCN(C)CC3)ccc1O) `ZINC001184252755.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184252755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184252755 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2Cc3cc(OC)c(OC)cc3C(=O)C23CCN(C)CC3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 11, 5, 5, 5, 10, 5, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [14, 10, 10, 10, 5, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 8, 20, 8, 8, 17, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 10, 10, 10, 10, 14, 14, 14, 10, 5, 5, 8, 8, 8, 20, 20, 20, 17, 17, 17, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 10, 10, 20] 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, 60, 61, 62, 63, 64]) total number of confs: 104 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 173) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/173: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2Cc3cc(OC)c(OC)cc3C(=O)C23CCN(C)CC3)ccc1O) `ZINC001184252755.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184252755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184252755 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2Cc3cc(OC)c(OC)cc3C(=O)C23CCN(C)CC3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 11, 5, 5, 5, 10, 5, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [14, 10, 10, 10, 5, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 8, 20, 8, 8, 17, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 10, 10, 10, 10, 14, 14, 14, 10, 5, 5, 8, 8, 8, 20, 20, 20, 17, 17, 17, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 10, 10, 20] 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, 60, 61, 62, 63, 64]) total number of confs: 104 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184252755 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755 Building ZINC001184252755 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184252755 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 170) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N2Cc3cc(OC)c(OC)cc3C(=O)C23CCN(C)CC3)ccc1O) `ZINC001184252755.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184252755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184252755 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2Cc3cc(OC)c(OC)cc3C(=O)C23CCN(C)CC3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 11, 5, 5, 5, 10, 5, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 10, 10, 10, 5, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 17, 7, 7, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 10, 10, 10, 10, 17, 17, 17, 10, 5, 5, 7, 7, 7, 17, 17, 17, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 10, 10, 20] 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, 60, 61, 62, 63, 64]) total number of confs: 98 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 171) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N2Cc3cc(OC)c(OC)cc3C(=O)C23CCN(C)CC3)ccc1O) `ZINC001184252755.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184252755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184252755 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2Cc3cc(OC)c(OC)cc3C(=O)C23CCN(C)CC3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 11, 5, 5, 5, 10, 5, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 10, 10, 10, 5, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 17, 7, 7, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 10, 10, 10, 10, 17, 17, 17, 10, 5, 5, 7, 7, 7, 17, 17, 17, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 10, 10, 20] 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, 60, 61, 62, 63, 64]) total number of confs: 98 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 172) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/172: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2Cc3cc(OC)c(OC)cc3C(=O)C23CCN(C)CC3)ccc1O) `ZINC001184252755.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184252755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184252755 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2Cc3cc(OC)c(OC)cc3C(=O)C23CCN(C)CC3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 11, 5, 5, 5, 10, 5, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [14, 10, 10, 10, 5, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 8, 20, 8, 8, 17, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 10, 10, 10, 10, 14, 14, 14, 10, 5, 5, 8, 8, 8, 20, 20, 20, 17, 17, 17, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 10, 10, 20] 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, 60, 61, 62, 63, 64]) total number of confs: 104 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 173) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/173: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2Cc3cc(OC)c(OC)cc3C(=O)C23CCN(C)CC3)ccc1O) `ZINC001184252755.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184252755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184252755 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2Cc3cc(OC)c(OC)cc3C(=O)C23CCN(C)CC3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 11, 5, 5, 5, 10, 5, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [14, 10, 10, 10, 5, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 8, 20, 8, 8, 17, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 10, 10, 10, 10, 14, 14, 14, 10, 5, 5, 8, 8, 8, 20, 20, 20, 17, 17, 17, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 10, 10, 20] 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, 60, 61, 62, 63, 64]) total number of confs: 104 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184252755 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184252755 Building ZINC001184253003 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253003' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253003 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184253003 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253003/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253003 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 174) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/174 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/174' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC(C(=O)N3CCN(c4ccccc4)CC3)CC2)ccc1O) `ZINC001184253003.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184253003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184253003 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC(C(=O)N3CCN(c4ccccc4)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.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 2, 1, 1, 1, 1, 2, 4, 6, 6, 6, 9, 18, 24, 24, 24, 24, 24, 30, 30, 30, 30, 30, 24, 24, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 6, 6, 6, 6, 6, 24, 24, 24, 24, 30, 30, 30, 30, 30, 24, 24, 24, 24, 6, 6, 6, 6, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 83 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253003 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253003/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253003 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 175) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/175 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/175' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC(C(=O)N3CCN(c4ccccc4)CC3)CC2)ccc1O) `ZINC001184253003.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184253003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253003/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184253003 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC(C(=O)N3CCN(c4ccccc4)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.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 2, 1, 1, 1, 1, 2, 4, 5, 5, 5, 8, 16, 18, 18, 18, 18, 18, 27, 27, 27, 27, 27, 18, 18, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 5, 5, 5, 5, 5, 18, 18, 18, 18, 27, 27, 27, 27, 27, 18, 18, 18, 18, 5, 5, 5, 5, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 81 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253003 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184253003 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253003/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253003/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253003 Building ZINC001184253003 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253003' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253003 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184253003 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253003/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253003 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 174) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC(C(=O)N3CCN(c4ccccc4)CC3)CC2)ccc1O) `ZINC001184253003.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184253003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184253003 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N2CCC(C(=O)N3CCN(c4ccccc4)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.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 2, 1, 1, 1, 1, 2, 4, 6, 6, 6, 9, 18, 24, 24, 24, 24, 24, 30, 30, 30, 30, 30, 24, 24, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 6, 6, 6, 6, 6, 24, 24, 24, 24, 30, 30, 30, 30, 30, 24, 24, 24, 24, 6, 6, 6, 6, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 83 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253003 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253003/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253003 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 175) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC(C(=O)N3CCN(c4ccccc4)CC3)CC2)ccc1O) `ZINC001184253003.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184253003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253003/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184253003 none COc1cc(C[C@]([O-])([SiH3])C(=O)N2CCC(C(=O)N3CCN(c4ccccc4)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.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 2, 1, 1, 1, 1, 2, 4, 5, 5, 5, 8, 16, 18, 18, 18, 18, 18, 27, 27, 27, 27, 27, 18, 18, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 5, 5, 5, 5, 5, 18, 18, 18, 18, 27, 27, 27, 27, 27, 18, 18, 18, 18, 5, 5, 5, 5, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 81 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253003 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184253003 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253003/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253003/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253003 Building ZINC001184253613 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253613' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253613 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184253613 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253613/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253613 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 176) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/176 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/176' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)S(=O)(=O)c1ccc(OC)c(NC(=O)[C@@]([O-])([SiH3])Cc2ccc(O)c(OC)c2)c1) `ZINC001184253613.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184253613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184253613 none CCN(CC)S(=O)(=O)c1ccc(OC)c(NC(=O)[C@@]([O-])([SiH3])Cc2ccc(O)c(OC)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [19, 14, 12, 14, 17, 3, 12, 12, 3, 2, 3, 3, 3, 5, 2, 2, 1, 2, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 6, 3, 3, 19, 19, 19, 19, 19, 17, 17, 17, 17, 17, 3, 3, 5, 5, 5, 2, 2, 2, 3, 3, 6, 6, 6, 6, 3, 3] 100 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: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253613 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253613/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253613 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 177) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/177 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/177' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)S(=O)(=O)c1ccc(OC)c(NC(=O)[C@]([O-])([SiH3])Cc2ccc(O)c(OC)c2)c1) `ZINC001184253613.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184253613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253613/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184253613 none CCN(CC)S(=O)(=O)c1ccc(OC)c(NC(=O)[C@]([O-])([SiH3])Cc2ccc(O)c(OC)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 14, 12, 14, 18, 3, 12, 12, 3, 3, 3, 3, 3, 5, 2, 2, 1, 2, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 7, 4, 3, 20, 20, 20, 20, 20, 18, 18, 18, 18, 18, 3, 3, 5, 5, 5, 2, 2, 2, 4, 4, 8, 7, 7, 7, 4, 3] 100 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253613 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184253613 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253613/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253613/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253613 Building ZINC001184253613 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253613' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253613 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184253613 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253613/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253613 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 176) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCN(CC)S(=O)(=O)c1ccc(OC)c(NC(=O)[C@@]([O-])([SiH3])Cc2ccc(O)c(OC)c2)c1) `ZINC001184253613.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184253613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184253613 none CCN(CC)S(=O)(=O)c1ccc(OC)c(NC(=O)[C@@]([O-])([SiH3])Cc2ccc(O)c(OC)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [19, 14, 12, 14, 17, 3, 12, 12, 3, 2, 3, 3, 3, 5, 2, 2, 1, 2, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 6, 3, 3, 19, 19, 19, 19, 19, 17, 17, 17, 17, 17, 3, 3, 5, 5, 5, 2, 2, 2, 3, 3, 6, 6, 6, 6, 3, 3] 100 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: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253613 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253613/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253613 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 177) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCN(CC)S(=O)(=O)c1ccc(OC)c(NC(=O)[C@]([O-])([SiH3])Cc2ccc(O)c(OC)c2)c1) `ZINC001184253613.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184253613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253613/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184253613 none CCN(CC)S(=O)(=O)c1ccc(OC)c(NC(=O)[C@]([O-])([SiH3])Cc2ccc(O)c(OC)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 14, 12, 14, 18, 3, 12, 12, 3, 3, 3, 3, 3, 5, 2, 2, 1, 2, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 7, 4, 3, 20, 20, 20, 20, 20, 18, 18, 18, 18, 18, 3, 3, 5, 5, 5, 2, 2, 2, 4, 4, 8, 7, 7, 7, 4, 3] 100 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253613 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184253613 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253613/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253613/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253613 Building ZINC001184253890 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253890' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253890 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184253890 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253890/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253890 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 178) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/178 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/178' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)NCc2ncn3c2CN(C(=O)OC(C)(C)C)CCC3)ccc1O) `ZINC001184253890.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184253890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184253890 none COc1cc(C[C@]([O-])([SiH3])C(=O)NCc2ncn3c2CN(C(=O)OC(C)(C)C)CCC3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 1, 8, 1, 8, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 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, 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, 6, 3, 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] 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, 6, 6, 6, 3, 1, 1, 1, 1, 3, 3, 3, 12, 15, 16, 16, 15, 16, 16, 16, 19, 19, 24, 24, 24, 24, 16, 16, 16, 6, 6, 6, 6, 15, 15, 15, 6, 3, 3, 3, 12, 12, 16, 16, 16, 24, 24, 24, 24, 24, 24, 24, 24, 24, 16, 16, 16, 16, 16, 16, 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, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253890 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253890/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253890 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 179) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/179 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/179' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)NCc2ncn3c2CN(C(=O)OC(C)(C)C)CCC3)ccc1O) `ZINC001184253890.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184253890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253890/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184253890 none COc1cc(C[C@@]([O-])([SiH3])C(=O)NCc2ncn3c2CN(C(=O)OC(C)(C)C)CCC3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 1, 8, 1, 8, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 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, 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, 6, 3, 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] 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: [12, 6, 6, 6, 3, 1, 1, 1, 1, 2, 2, 2, 13, 11, 16, 16, 16, 16, 16, 16, 19, 19, 23, 23, 23, 23, 16, 16, 16, 6, 6, 6, 6, 12, 12, 12, 6, 3, 3, 2, 8, 8, 16, 16, 16, 23, 23, 23, 23, 23, 23, 23, 23, 23, 16, 16, 16, 16, 16, 16, 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, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 99 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253890 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184253890 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253890/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253890/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253890 Building ZINC001184253890 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253890' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253890 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184253890 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253890/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253890 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 178) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)NCc2ncn3c2CN(C(=O)OC(C)(C)C)CCC3)ccc1O) `ZINC001184253890.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184253890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184253890 none COc1cc(C[C@]([O-])([SiH3])C(=O)NCc2ncn3c2CN(C(=O)OC(C)(C)C)CCC3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 1, 8, 1, 8, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 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, 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, 6, 3, 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] 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, 6, 6, 6, 3, 1, 1, 1, 1, 3, 3, 3, 12, 15, 16, 16, 15, 16, 16, 16, 19, 19, 24, 24, 24, 24, 16, 16, 16, 6, 6, 6, 6, 15, 15, 15, 6, 3, 3, 3, 12, 12, 16, 16, 16, 24, 24, 24, 24, 24, 24, 24, 24, 24, 16, 16, 16, 16, 16, 16, 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, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253890 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253890/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253890 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 179) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)NCc2ncn3c2CN(C(=O)OC(C)(C)C)CCC3)ccc1O) `ZINC001184253890.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184253890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253890/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184253890 none COc1cc(C[C@@]([O-])([SiH3])C(=O)NCc2ncn3c2CN(C(=O)OC(C)(C)C)CCC3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 1, 8, 1, 8, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 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, 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, 6, 3, 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] 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: [12, 6, 6, 6, 3, 1, 1, 1, 1, 2, 2, 2, 13, 11, 16, 16, 16, 16, 16, 16, 19, 19, 23, 23, 23, 23, 16, 16, 16, 6, 6, 6, 6, 12, 12, 12, 6, 3, 3, 2, 8, 8, 16, 16, 16, 23, 23, 23, 23, 23, 23, 23, 23, 23, 16, 16, 16, 16, 16, 16, 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, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 99 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253890 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184253890 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253890/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253890/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253890 Building ZINC001184253893 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253893' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253893 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184253893 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253893/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253893 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 180) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/180 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/180' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@H](CC(=O)OC(C)(C)C)OC(C)(C)O2)ccc1O) `ZINC001184253893.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184253893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253893/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184253893 none COc1cc(C[C@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@H](CC(=O)OC(C)(C)C)OC(C)(C)O2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 1, 11, 12, 5, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 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, 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, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 4, 6, 6, 6, 6, 6, 15, 36, 36, 39, 39, 39, 39, 6, 6, 6, 6, 6, 5, 5, 5, 5, 9, 9, 9, 5, 3, 3, 1, 4, 4, 6, 6, 15, 15, 39, 39, 39, 39, 39, 39, 39, 39, 39, 6, 6, 6, 6, 6, 6, 5, 5, 10] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 40] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253893 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253893/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253893 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 181) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/181 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/181' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@H](CC(=O)OC(C)(C)C)OC(C)(C)O2)ccc1O) `ZINC001184253893.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184253893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253893/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184253893 none COc1cc(C[C@@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@H](CC(=O)OC(C)(C)C)OC(C)(C)O2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 1, 11, 12, 5, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 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, 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, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 3, 2, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 19, 39, 39, 39, 39, 39, 39, 7, 7, 7, 7, 7, 3, 3, 3, 3, 6, 6, 6, 3, 2, 2, 1, 5, 5, 7, 7, 19, 19, 39, 39, 39, 39, 39, 39, 39, 39, 39, 7, 7, 7, 7, 7, 7, 3, 3, 6] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 40] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253893 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184253893 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253893/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253893/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253893 Building ZINC001184253893 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253893' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253893 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184253893 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253893/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253893 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 180) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@H](CC(=O)OC(C)(C)C)OC(C)(C)O2)ccc1O) `ZINC001184253893.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184253893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253893/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184253893 none COc1cc(C[C@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@H](CC(=O)OC(C)(C)C)OC(C)(C)O2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 1, 11, 12, 5, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 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, 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, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 4, 6, 6, 6, 6, 6, 15, 36, 36, 39, 39, 39, 39, 6, 6, 6, 6, 6, 5, 5, 5, 5, 9, 9, 9, 5, 3, 3, 1, 4, 4, 6, 6, 15, 15, 39, 39, 39, 39, 39, 39, 39, 39, 39, 6, 6, 6, 6, 6, 6, 5, 5, 10] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 40] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253893 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253893/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253893 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 181) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@H](CC(=O)OC(C)(C)C)OC(C)(C)O2)ccc1O) `ZINC001184253893.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184253893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253893/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184253893 none COc1cc(C[C@@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@H](CC(=O)OC(C)(C)C)OC(C)(C)O2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 1, 11, 12, 5, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 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, 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, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 3, 2, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 19, 39, 39, 39, 39, 39, 39, 7, 7, 7, 7, 7, 3, 3, 3, 3, 6, 6, 6, 3, 2, 2, 1, 5, 5, 7, 7, 19, 19, 39, 39, 39, 39, 39, 39, 39, 39, 39, 7, 7, 7, 7, 7, 7, 3, 3, 6] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 40] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253893 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184253893 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253893/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253893/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253893 Building ZINC001184253927 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253927' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253927 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184253927 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253927/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253927 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 182) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/182 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/182' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2cc3cccc4c3c(c2)C(=O)N(CCN(C)C)C4=O)ccc1O) `ZINC001184253927.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184253927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184253927 none COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2cc3cccc4c3c(c2)C(=O)N(CCN(C)C)C4=O)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', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 10, 5, 5, 1, 11, 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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 18, 18, 25, 25, 9, 9, 4, 4, 4, 4, 8, 8, 8, 4, 2, 2, 2, 9, 9, 9, 9, 9, 18, 18, 18, 18, 25, 25, 25, 25, 25, 25, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253927 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253927/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253927 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 183) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/183 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/183' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2cc3cccc4c3c(c2)C(=O)N(CCN(C)C)C4=O)ccc1O) `ZINC001184253927.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184253927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253927/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184253927 none COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2cc3cccc4c3c(c2)C(=O)N(CCN(C)C)C4=O)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', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 10, 5, 5, 1, 11, 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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 18, 18, 25, 25, 9, 9, 4, 4, 4, 4, 8, 8, 8, 4, 2, 2, 2, 9, 9, 9, 9, 9, 18, 18, 18, 18, 25, 25, 25, 25, 25, 25, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253927 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184253927 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253927/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253927/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253927 Building ZINC001184253927 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253927' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253927 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184253927 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253927/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253927 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 182) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2cc3cccc4c3c(c2)C(=O)N(CCN(C)C)C4=O)ccc1O) `ZINC001184253927.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184253927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184253927 none COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2cc3cccc4c3c(c2)C(=O)N(CCN(C)C)C4=O)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', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 10, 5, 5, 1, 11, 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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 18, 18, 25, 25, 9, 9, 4, 4, 4, 4, 8, 8, 8, 4, 2, 2, 2, 9, 9, 9, 9, 9, 18, 18, 18, 18, 25, 25, 25, 25, 25, 25, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253927 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253927/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253927 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 183) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2cc3cccc4c3c(c2)C(=O)N(CCN(C)C)C4=O)ccc1O) `ZINC001184253927.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184253927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253927/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184253927 none COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2cc3cccc4c3c(c2)C(=O)N(CCN(C)C)C4=O)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', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 10, 5, 5, 1, 11, 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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 18, 18, 25, 25, 9, 9, 4, 4, 4, 4, 8, 8, 8, 4, 2, 2, 2, 9, 9, 9, 9, 9, 18, 18, 18, 18, 25, 25, 25, 25, 25, 25, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253927 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184253927 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253927/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253927/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184253927 Building ZINC001184254313 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254313' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254313 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184254313 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254313/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254313 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 184) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/184 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/184' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=C(NC(=O)[C@@]([O-])([SiH3])Cc2ccc(O)c(OC)c2)CCN(C(=O)OC(C)(C)C)C1) `ZINC001184254313.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184254313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254313/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184254313 none CCOC(=O)C1=C(NC(=O)[C@@]([O-])([SiH3])Cc2ccc(O)c(OC)c2)CCN(C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 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] 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, 9, 4, 9, 4, 2, 2, 1, 2, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 13, 6, 4, 4, 4, 4, 9, 9, 13, 13, 13, 13, 4, 15, 15, 15, 15, 15, 2, 3, 3, 6, 6, 12, 13, 13, 13, 6, 4, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4, 4] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254313 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254313/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254313 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 185) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/185 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/185' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=C(NC(=O)[C@]([O-])([SiH3])Cc2ccc(O)c(OC)c2)CCN(C(=O)OC(C)(C)C)C1) `ZINC001184254313.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184254313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254313/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184254313 none CCOC(=O)C1=C(NC(=O)[C@]([O-])([SiH3])Cc2ccc(O)c(OC)c2)CCN(C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [14, 9, 9, 4, 9, 4, 2, 2, 1, 2, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 12, 6, 4, 4, 4, 4, 9, 9, 12, 12, 12, 12, 4, 14, 14, 14, 14, 14, 2, 3, 3, 6, 6, 12, 12, 12, 12, 6, 4, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254313 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184254313 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254313/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254313/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254313 Building ZINC001184254313 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254313' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254313 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184254313 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254313/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254313 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 184) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCOC(=O)C1=C(NC(=O)[C@@]([O-])([SiH3])Cc2ccc(O)c(OC)c2)CCN(C(=O)OC(C)(C)C)C1) `ZINC001184254313.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184254313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254313/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184254313 none CCOC(=O)C1=C(NC(=O)[C@@]([O-])([SiH3])Cc2ccc(O)c(OC)c2)CCN(C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 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] 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, 9, 4, 9, 4, 2, 2, 1, 2, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 13, 6, 4, 4, 4, 4, 9, 9, 13, 13, 13, 13, 4, 15, 15, 15, 15, 15, 2, 3, 3, 6, 6, 12, 13, 13, 13, 6, 4, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4, 4] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254313 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254313/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254313 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 185) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCOC(=O)C1=C(NC(=O)[C@]([O-])([SiH3])Cc2ccc(O)c(OC)c2)CCN(C(=O)OC(C)(C)C)C1) `ZINC001184254313.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184254313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254313/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184254313 none CCOC(=O)C1=C(NC(=O)[C@]([O-])([SiH3])Cc2ccc(O)c(OC)c2)CCN(C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [14, 9, 9, 4, 9, 4, 2, 2, 1, 2, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 12, 6, 4, 4, 4, 4, 9, 9, 12, 12, 12, 12, 4, 14, 14, 14, 14, 14, 2, 3, 3, 6, 6, 12, 12, 12, 12, 6, 4, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254313 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184254313 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254313/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254313/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254313 Building ZINC001184254659 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254659' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254659 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184254659 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254659/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254659 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 186) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/186 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/186' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2c(Br)c(O)nc(=O)n2Cc2ccccc2)ccc1O) `ZINC001184254659.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184254659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184254659 none COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2c(Br)c(O)nc(=O)n2Cc2ccccc2)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', 'Br', 'C.2', 'O.3', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 17, 1, 12, 8, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 6, 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, 4, 7, 7, 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] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [23, 9, 9, 9, 5, 1, 1, 1, 1, 3, 3, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 12, 19, 19, 13, 19, 19, 9, 9, 9, 9, 23, 23, 23, 9, 5, 5, 4, 30, 12, 12, 19, 19, 18, 19, 19, 9, 9, 18] 300 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 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: 156 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254659 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254659/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254659 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 187) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/187 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/187' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2c(Br)c(O)nc(=O)n2Cc2ccccc2)ccc1O) `ZINC001184254659.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184254659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254659/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184254659 none COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2c(Br)c(O)nc(=O)n2Cc2ccccc2)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', 'Br', 'C.2', 'O.3', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 17, 1, 12, 8, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 6, 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, 4, 7, 7, 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] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [24, 9, 9, 9, 5, 1, 1, 1, 1, 3, 3, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 12, 19, 19, 14, 19, 19, 9, 9, 9, 9, 24, 24, 24, 9, 5, 5, 4, 30, 12, 12, 19, 19, 19, 19, 19, 9, 9, 18] 300 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 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: 156 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254659 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184254659 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254659/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254659/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254659 Building ZINC001184254659 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254659' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254659 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184254659 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254659/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254659 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 186) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2c(Br)c(O)nc(=O)n2Cc2ccccc2)ccc1O) `ZINC001184254659.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184254659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184254659 none COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2c(Br)c(O)nc(=O)n2Cc2ccccc2)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', 'Br', 'C.2', 'O.3', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 17, 1, 12, 8, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 6, 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, 4, 7, 7, 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] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [23, 9, 9, 9, 5, 1, 1, 1, 1, 3, 3, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 12, 19, 19, 13, 19, 19, 9, 9, 9, 9, 23, 23, 23, 9, 5, 5, 4, 30, 12, 12, 19, 19, 18, 19, 19, 9, 9, 18] 300 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 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: 156 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254659 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254659/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254659 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 187) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2c(Br)c(O)nc(=O)n2Cc2ccccc2)ccc1O) `ZINC001184254659.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184254659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254659/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184254659 none COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2c(Br)c(O)nc(=O)n2Cc2ccccc2)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', 'Br', 'C.2', 'O.3', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 17, 1, 12, 8, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 6, 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, 4, 7, 7, 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] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [24, 9, 9, 9, 5, 1, 1, 1, 1, 3, 3, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 12, 19, 19, 14, 19, 19, 9, 9, 9, 9, 24, 24, 24, 9, 5, 5, 4, 30, 12, 12, 19, 19, 19, 19, 19, 9, 9, 18] 300 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 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: 156 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254659 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184254659 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254659/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254659/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254659 Building ZINC001184254915 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184254915 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 188) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/188 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/188' -> `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]2CC[N@](C3CCN(C(=O)OC(C)(C)C)CC3)CC2)ccc1O) `ZINC001184254915.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184254915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 74 natoms 73 natoms 72 natoms 71 names: ZINC001184254915 none COc1cc(C[C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](C3CCN(C(=O)OC(C)(C)C)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.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 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, 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, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 18, 18, 18, 18, 28, 28, 28, 28, 28, 28, 18, 18, 6, 6, 4, 4, 4, 4, 10, 10, 10, 4, 2, 2, 1, 6, 6, 6, 6, 18, 18, 18, 18, 18, 28, 28, 28, 28, 28, 28, 28, 28, 28, 18, 18, 18, 18, 6, 6, 6, 6, 4, 4, 8] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 41] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 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, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 115 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 189) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/189 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/189' -> `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]2CC[N@@](C3CCN(C(=O)OC(C)(C)C)CC3)CC2)ccc1O) `ZINC001184254915.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184254915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 74 natoms 73 natoms 72 natoms 71 names: ZINC001184254915 none COc1cc(C[C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](C3CCN(C(=O)OC(C)(C)C)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.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 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, 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, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 18, 18, 18, 18, 28, 28, 28, 28, 28, 28, 18, 18, 6, 6, 4, 4, 4, 4, 10, 10, 10, 4, 2, 2, 1, 6, 6, 6, 6, 18, 18, 18, 18, 18, 28, 28, 28, 28, 28, 28, 28, 28, 28, 18, 18, 18, 18, 6, 6, 6, 6, 4, 4, 8] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 41] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 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, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 115 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 190) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/190 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/190' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](C3CCN(C(=O)OC(C)(C)C)CC3)CC2)ccc1O) `ZINC001184254915.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184254915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 74 natoms 73 natoms 72 natoms 71 names: ZINC001184254915 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](C3CCN(C(=O)OC(C)(C)C)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.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 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, 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, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 17, 17, 17, 17, 28, 28, 28, 28, 28, 28, 17, 17, 6, 6, 4, 4, 4, 4, 10, 10, 10, 4, 2, 2, 1, 6, 6, 6, 6, 17, 17, 17, 17, 17, 28, 28, 28, 28, 28, 28, 28, 28, 28, 17, 17, 17, 17, 6, 6, 6, 6, 4, 4, 8] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 41] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 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, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 115 number of broken/clashed sets: 68 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 191) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/191 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/191' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](C3CCN(C(=O)OC(C)(C)C)CC3)CC2)ccc1O) `ZINC001184254915.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184254915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 74 natoms 73 natoms 72 natoms 71 names: ZINC001184254915 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](C3CCN(C(=O)OC(C)(C)C)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.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 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, 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, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 17, 17, 17, 17, 28, 28, 28, 28, 28, 28, 17, 17, 6, 6, 4, 4, 4, 4, 10, 10, 10, 4, 2, 2, 1, 6, 6, 6, 6, 17, 17, 17, 17, 17, 28, 28, 28, 28, 28, 28, 28, 28, 28, 17, 17, 17, 17, 6, 6, 6, 6, 4, 4, 8] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 41] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 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, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 115 number of broken/clashed sets: 68 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184254915 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915 Building ZINC001184254915 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184254915 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 188) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](C3CCN(C(=O)OC(C)(C)C)CC3)CC2)ccc1O) `ZINC001184254915.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184254915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 74 natoms 73 natoms 72 natoms 71 names: ZINC001184254915 none COc1cc(C[C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](C3CCN(C(=O)OC(C)(C)C)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.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 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, 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, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 18, 18, 18, 18, 28, 28, 28, 28, 28, 28, 18, 18, 6, 6, 4, 4, 4, 4, 10, 10, 10, 4, 2, 2, 1, 6, 6, 6, 6, 18, 18, 18, 18, 18, 28, 28, 28, 28, 28, 28, 28, 28, 28, 18, 18, 18, 18, 6, 6, 6, 6, 4, 4, 8] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 41] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 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, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 115 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 189) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](C3CCN(C(=O)OC(C)(C)C)CC3)CC2)ccc1O) `ZINC001184254915.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184254915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 74 natoms 73 natoms 72 natoms 71 names: ZINC001184254915 none COc1cc(C[C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](C3CCN(C(=O)OC(C)(C)C)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.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 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, 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, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 18, 18, 18, 18, 28, 28, 28, 28, 28, 28, 18, 18, 6, 6, 4, 4, 4, 4, 10, 10, 10, 4, 2, 2, 1, 6, 6, 6, 6, 18, 18, 18, 18, 18, 28, 28, 28, 28, 28, 28, 28, 28, 28, 18, 18, 18, 18, 6, 6, 6, 6, 4, 4, 8] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 41] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 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, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 115 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 190) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/190: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]2CC[N@](C3CCN(C(=O)OC(C)(C)C)CC3)CC2)ccc1O) `ZINC001184254915.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184254915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 74 natoms 73 natoms 72 natoms 71 names: ZINC001184254915 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](C3CCN(C(=O)OC(C)(C)C)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.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 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, 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, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 17, 17, 17, 17, 28, 28, 28, 28, 28, 28, 17, 17, 6, 6, 4, 4, 4, 4, 10, 10, 10, 4, 2, 2, 1, 6, 6, 6, 6, 17, 17, 17, 17, 17, 28, 28, 28, 28, 28, 28, 28, 28, 28, 17, 17, 17, 17, 6, 6, 6, 6, 4, 4, 8] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 41] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 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, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 115 number of broken/clashed sets: 68 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 191) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/191: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]2CC[N@@](C3CCN(C(=O)OC(C)(C)C)CC3)CC2)ccc1O) `ZINC001184254915.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184254915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 74 natoms 73 natoms 72 natoms 71 names: ZINC001184254915 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](C3CCN(C(=O)OC(C)(C)C)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.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 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, 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, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 17, 17, 17, 17, 28, 28, 28, 28, 28, 28, 17, 17, 6, 6, 4, 4, 4, 4, 10, 10, 10, 4, 2, 2, 1, 6, 6, 6, 6, 17, 17, 17, 17, 17, 28, 28, 28, 28, 28, 28, 28, 28, 28, 17, 17, 17, 17, 6, 6, 6, 6, 4, 4, 8] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 41] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 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, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 115 number of broken/clashed sets: 68 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184254915 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915 Building ZINC001184254915 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184254915 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 188) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](C3CCN(C(=O)OC(C)(C)C)CC3)CC2)ccc1O) `ZINC001184254915.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184254915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 74 natoms 73 natoms 72 natoms 71 names: ZINC001184254915 none COc1cc(C[C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](C3CCN(C(=O)OC(C)(C)C)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.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 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, 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, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 18, 18, 18, 18, 28, 28, 28, 28, 28, 28, 18, 18, 6, 6, 4, 4, 4, 4, 10, 10, 10, 4, 2, 2, 1, 6, 6, 6, 6, 18, 18, 18, 18, 18, 28, 28, 28, 28, 28, 28, 28, 28, 28, 18, 18, 18, 18, 6, 6, 6, 6, 4, 4, 8] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 41] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 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, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 115 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 189) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](C3CCN(C(=O)OC(C)(C)C)CC3)CC2)ccc1O) `ZINC001184254915.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184254915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 74 natoms 73 natoms 72 natoms 71 names: ZINC001184254915 none COc1cc(C[C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](C3CCN(C(=O)OC(C)(C)C)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.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 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, 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, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 18, 18, 18, 18, 28, 28, 28, 28, 28, 28, 18, 18, 6, 6, 4, 4, 4, 4, 10, 10, 10, 4, 2, 2, 1, 6, 6, 6, 6, 18, 18, 18, 18, 18, 28, 28, 28, 28, 28, 28, 28, 28, 28, 18, 18, 18, 18, 6, 6, 6, 6, 4, 4, 8] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 41] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 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, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 115 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 190) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/190: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]2CC[N@](C3CCN(C(=O)OC(C)(C)C)CC3)CC2)ccc1O) `ZINC001184254915.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184254915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 74 natoms 73 natoms 72 natoms 71 names: ZINC001184254915 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](C3CCN(C(=O)OC(C)(C)C)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.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 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, 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, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 17, 17, 17, 17, 28, 28, 28, 28, 28, 28, 17, 17, 6, 6, 4, 4, 4, 4, 10, 10, 10, 4, 2, 2, 1, 6, 6, 6, 6, 17, 17, 17, 17, 17, 28, 28, 28, 28, 28, 28, 28, 28, 28, 17, 17, 17, 17, 6, 6, 6, 6, 4, 4, 8] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 41] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 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, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 115 number of broken/clashed sets: 68 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 191) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/191: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]2CC[N@@](C3CCN(C(=O)OC(C)(C)C)CC3)CC2)ccc1O) `ZINC001184254915.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184254915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 74 natoms 73 natoms 72 natoms 71 names: ZINC001184254915 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](C3CCN(C(=O)OC(C)(C)C)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.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 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, 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, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 17, 17, 17, 17, 28, 28, 28, 28, 28, 28, 17, 17, 6, 6, 4, 4, 4, 4, 10, 10, 10, 4, 2, 2, 1, 6, 6, 6, 6, 17, 17, 17, 17, 17, 28, 28, 28, 28, 28, 28, 28, 28, 28, 17, 17, 17, 17, 6, 6, 6, 6, 4, 4, 8] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 41] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 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, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 115 number of broken/clashed sets: 68 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184254915 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915 Building ZINC001184254915 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184254915 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 188) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](C3CCN(C(=O)OC(C)(C)C)CC3)CC2)ccc1O) `ZINC001184254915.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184254915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 74 natoms 73 natoms 72 natoms 71 names: ZINC001184254915 none COc1cc(C[C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](C3CCN(C(=O)OC(C)(C)C)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.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 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, 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, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 18, 18, 18, 18, 28, 28, 28, 28, 28, 28, 18, 18, 6, 6, 4, 4, 4, 4, 10, 10, 10, 4, 2, 2, 1, 6, 6, 6, 6, 18, 18, 18, 18, 18, 28, 28, 28, 28, 28, 28, 28, 28, 28, 18, 18, 18, 18, 6, 6, 6, 6, 4, 4, 8] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 41] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 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, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 115 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 189) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](C3CCN(C(=O)OC(C)(C)C)CC3)CC2)ccc1O) `ZINC001184254915.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184254915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 74 natoms 73 natoms 72 natoms 71 names: ZINC001184254915 none COc1cc(C[C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](C3CCN(C(=O)OC(C)(C)C)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.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 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, 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, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 18, 18, 18, 18, 28, 28, 28, 28, 28, 28, 18, 18, 6, 6, 4, 4, 4, 4, 10, 10, 10, 4, 2, 2, 1, 6, 6, 6, 6, 18, 18, 18, 18, 18, 28, 28, 28, 28, 28, 28, 28, 28, 28, 18, 18, 18, 18, 6, 6, 6, 6, 4, 4, 8] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 41] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 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, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 115 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 190) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/190: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]2CC[N@](C3CCN(C(=O)OC(C)(C)C)CC3)CC2)ccc1O) `ZINC001184254915.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184254915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 74 natoms 73 natoms 72 natoms 71 names: ZINC001184254915 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](C3CCN(C(=O)OC(C)(C)C)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.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 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, 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, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 17, 17, 17, 17, 28, 28, 28, 28, 28, 28, 17, 17, 6, 6, 4, 4, 4, 4, 10, 10, 10, 4, 2, 2, 1, 6, 6, 6, 6, 17, 17, 17, 17, 17, 28, 28, 28, 28, 28, 28, 28, 28, 28, 17, 17, 17, 17, 6, 6, 6, 6, 4, 4, 8] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 41] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 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, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 115 number of broken/clashed sets: 68 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 191) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/191: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]2CC[N@@](C3CCN(C(=O)OC(C)(C)C)CC3)CC2)ccc1O) `ZINC001184254915.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184254915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 74 natoms 73 natoms 72 natoms 71 names: ZINC001184254915 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](C3CCN(C(=O)OC(C)(C)C)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.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 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, 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, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 17, 17, 17, 17, 28, 28, 28, 28, 28, 28, 17, 17, 6, 6, 4, 4, 4, 4, 10, 10, 10, 4, 2, 2, 1, 6, 6, 6, 6, 17, 17, 17, 17, 17, 28, 28, 28, 28, 28, 28, 28, 28, 28, 17, 17, 17, 17, 6, 6, 6, 6, 4, 4, 8] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 41] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 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, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 115 number of broken/clashed sets: 68 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184254915 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184254915 Building ZINC001184255159 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255159' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255159 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184255159 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255159/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255159 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 192) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/192 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/192' -> `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]2CCc3c(ccc(=O)n3Cc3cccc(C)n3)C2)ccc1O) `ZINC001184255159.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184255159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184255159 none COc1cc(C[C@]([O-])([SiH3])C(=O)N[C@H]2CCc3c(ccc(=O)n3Cc3cccc(C)n3)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.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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: [7, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 14, 27, 27, 27, 27, 27, 27, 7, 4, 4, 4, 4, 7, 7, 7, 4, 2, 2, 1, 7, 7, 7, 7, 7, 7, 14, 14, 27, 27, 27, 27, 27, 27, 7, 7, 4, 4, 8] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 41] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 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: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255159 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255159/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255159 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 193) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/193 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/193' -> `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]2CCc3c(ccc(=O)n3Cc3cccc(C)n3)C2)ccc1O) `ZINC001184255159.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184255159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255159/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184255159 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N[C@H]2CCc3c(ccc(=O)n3Cc3cccc(C)n3)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.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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: [7, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 12, 30, 30, 30, 30, 30, 30, 7, 4, 4, 4, 4, 7, 7, 7, 4, 2, 2, 1, 7, 7, 7, 7, 7, 7, 12, 12, 30, 30, 30, 30, 30, 30, 7, 7, 4, 4, 8] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 41] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 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: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255159 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184255159 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255159/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255159/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255159 Building ZINC001184255159 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255159' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255159 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184255159 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255159/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255159 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 192) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N[C@H]2CCc3c(ccc(=O)n3Cc3cccc(C)n3)C2)ccc1O) `ZINC001184255159.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184255159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184255159 none COc1cc(C[C@]([O-])([SiH3])C(=O)N[C@H]2CCc3c(ccc(=O)n3Cc3cccc(C)n3)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.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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: [7, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 14, 27, 27, 27, 27, 27, 27, 7, 4, 4, 4, 4, 7, 7, 7, 4, 2, 2, 1, 7, 7, 7, 7, 7, 7, 14, 14, 27, 27, 27, 27, 27, 27, 7, 7, 4, 4, 8] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 41] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 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: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255159 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255159/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255159 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 193) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)N[C@H]2CCc3c(ccc(=O)n3Cc3cccc(C)n3)C2)ccc1O) `ZINC001184255159.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184255159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255159/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184255159 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N[C@H]2CCc3c(ccc(=O)n3Cc3cccc(C)n3)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.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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: [7, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 12, 30, 30, 30, 30, 30, 30, 7, 4, 4, 4, 4, 7, 7, 7, 4, 2, 2, 1, 7, 7, 7, 7, 7, 7, 12, 12, 30, 30, 30, 30, 30, 30, 7, 7, 4, 4, 8] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 41] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 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: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255159 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184255159 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255159/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255159/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255159 Building ZINC001184255160 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255160' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255160 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184255160 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255160/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255160 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 194) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/194 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/194' -> `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]2CCc3c(ccc(=O)n3Cc3cccc(C)n3)C2)ccc1O) `ZINC001184255160.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184255160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184255160 none COc1cc(C[C@]([O-])([SiH3])C(=O)N[C@@H]2CCc3c(ccc(=O)n3Cc3cccc(C)n3)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.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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: [7, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 12, 30, 30, 30, 30, 30, 30, 7, 4, 4, 4, 4, 7, 7, 7, 4, 2, 2, 1, 7, 7, 7, 7, 7, 7, 12, 12, 30, 30, 30, 30, 30, 30, 7, 7, 4, 4, 8] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 41] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 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: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255160 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255160/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255160 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 195) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/195 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/195' -> `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]2CCc3c(ccc(=O)n3Cc3cccc(C)n3)C2)ccc1O) `ZINC001184255160.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184255160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255160/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184255160 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N[C@@H]2CCc3c(ccc(=O)n3Cc3cccc(C)n3)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.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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: [7, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 14, 26, 26, 26, 26, 26, 26, 7, 4, 4, 4, 4, 7, 7, 7, 4, 2, 2, 1, 7, 7, 7, 7, 7, 7, 14, 14, 26, 26, 26, 26, 26, 26, 7, 7, 4, 4, 8] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 41] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 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: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255160 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184255160 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255160/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255160/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255160 Building ZINC001184255160 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255160' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255160 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184255160 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255160/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255160 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 194) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N[C@@H]2CCc3c(ccc(=O)n3Cc3cccc(C)n3)C2)ccc1O) `ZINC001184255160.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184255160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184255160 none COc1cc(C[C@]([O-])([SiH3])C(=O)N[C@@H]2CCc3c(ccc(=O)n3Cc3cccc(C)n3)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.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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: [7, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 12, 30, 30, 30, 30, 30, 30, 7, 4, 4, 4, 4, 7, 7, 7, 4, 2, 2, 1, 7, 7, 7, 7, 7, 7, 12, 12, 30, 30, 30, 30, 30, 30, 7, 7, 4, 4, 8] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 41] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 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: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255160 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255160/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255160 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 195) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)N[C@@H]2CCc3c(ccc(=O)n3Cc3cccc(C)n3)C2)ccc1O) `ZINC001184255160.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184255160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255160/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184255160 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N[C@@H]2CCc3c(ccc(=O)n3Cc3cccc(C)n3)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.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 8, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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: [7, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 14, 26, 26, 26, 26, 26, 26, 7, 4, 4, 4, 4, 7, 7, 7, 4, 2, 2, 1, 7, 7, 7, 7, 7, 7, 14, 14, 26, 26, 26, 26, 26, 26, 7, 7, 4, 4, 8] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 41] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 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: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255160 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184255160 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255160/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255160/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255160 Building ZINC001184255183 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255183' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255183 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184255183 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255183/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255183 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 196) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/196 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/196' -> `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]2CCS(=O)(=O)c3ccc(Br)cc32)ccc1O) `ZINC001184255183.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184255183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184255183 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N[C@H]2CCS(=O)(=O)c3ccc(Br)cc32)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [17, 9, 9, 9, 5, 1, 1, 1, 1, 3, 3, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 9, 9, 9, 9, 17, 17, 17, 9, 5, 5, 3, 10, 10, 10, 10, 10, 10, 10, 9, 9, 18] 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: 85 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255183 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255183/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255183 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 197) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/197 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/197' -> `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]2CCS(=O)(=O)c3ccc(Br)cc32)ccc1O) `ZINC001184255183.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184255183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255183/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184255183 none COc1cc(C[C@]([O-])([SiH3])C(=O)N[C@H]2CCS(=O)(=O)c3ccc(Br)cc32)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [21, 13, 13, 13, 7, 1, 1, 1, 1, 3, 3, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 13, 13, 13, 13, 21, 21, 21, 13, 7, 7, 3, 11, 11, 11, 11, 11, 11, 11, 13, 13, 26] 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: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255183 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184255183 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255183/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255183/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255183 Building ZINC001184255183 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255183' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255183 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184255183 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255183/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255183 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 196) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)N[C@H]2CCS(=O)(=O)c3ccc(Br)cc32)ccc1O) `ZINC001184255183.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184255183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184255183 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N[C@H]2CCS(=O)(=O)c3ccc(Br)cc32)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [17, 9, 9, 9, 5, 1, 1, 1, 1, 3, 3, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 9, 9, 9, 9, 17, 17, 17, 9, 5, 5, 3, 10, 10, 10, 10, 10, 10, 10, 9, 9, 18] 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: 85 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255183 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255183/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255183 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 197) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N[C@H]2CCS(=O)(=O)c3ccc(Br)cc32)ccc1O) `ZINC001184255183.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184255183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255183/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184255183 none COc1cc(C[C@]([O-])([SiH3])C(=O)N[C@H]2CCS(=O)(=O)c3ccc(Br)cc32)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [21, 13, 13, 13, 7, 1, 1, 1, 1, 3, 3, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 13, 13, 13, 13, 21, 21, 21, 13, 7, 7, 3, 11, 11, 11, 11, 11, 11, 11, 13, 13, 26] 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: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255183 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184255183 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255183/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255183/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255183 Building ZINC001184255184 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255184' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255184 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184255184 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255184/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255184 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 198) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/198 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/198' -> `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]2CCS(=O)(=O)c3ccc(Br)cc32)ccc1O) `ZINC001184255184.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184255184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255184/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184255184 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N[C@@H]2CCS(=O)(=O)c3ccc(Br)cc32)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [21, 13, 13, 13, 7, 1, 1, 1, 1, 3, 3, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 13, 13, 13, 13, 21, 21, 21, 13, 7, 7, 3, 11, 11, 11, 11, 11, 11, 11, 13, 13, 26] 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: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255184 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255184/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255184 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 199) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/199 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/199' -> `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]2CCS(=O)(=O)c3ccc(Br)cc32)ccc1O) `ZINC001184255184.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184255184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255184/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184255184 none COc1cc(C[C@]([O-])([SiH3])C(=O)N[C@@H]2CCS(=O)(=O)c3ccc(Br)cc32)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [17, 9, 9, 9, 5, 1, 1, 1, 1, 3, 3, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 9, 9, 9, 9, 17, 17, 17, 9, 5, 5, 3, 10, 10, 10, 10, 10, 10, 10, 9, 9, 18] 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: 85 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255184 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184255184 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255184/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255184/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255184 Building ZINC001184255184 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255184' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255184 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184255184 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255184/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255184 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 198) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)N[C@@H]2CCS(=O)(=O)c3ccc(Br)cc32)ccc1O) `ZINC001184255184.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184255184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255184/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184255184 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N[C@@H]2CCS(=O)(=O)c3ccc(Br)cc32)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [21, 13, 13, 13, 7, 1, 1, 1, 1, 3, 3, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 13, 13, 13, 13, 21, 21, 21, 13, 7, 7, 3, 11, 11, 11, 11, 11, 11, 11, 13, 13, 26] 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: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255184 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255184/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255184 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 199) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N[C@@H]2CCS(=O)(=O)c3ccc(Br)cc32)ccc1O) `ZINC001184255184.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184255184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255184/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184255184 none COc1cc(C[C@]([O-])([SiH3])C(=O)N[C@@H]2CCS(=O)(=O)c3ccc(Br)cc32)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [17, 9, 9, 9, 5, 1, 1, 1, 1, 3, 3, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 9, 9, 9, 9, 17, 17, 17, 9, 5, 5, 3, 10, 10, 10, 10, 10, 10, 10, 9, 9, 18] 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: 85 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255184 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184255184 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255184/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255184/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255184 Building ZINC001184255474 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184255474 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 200) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/200 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/200' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2ccc(OC)c(OCCC[N@]3CC[N@](C)CC3)c2)ccc1O) `ZINC001184255474.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184255474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184255474 none COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2ccc(OC)c(OCCC[N@]3CC[N@](C)CC3)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', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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', '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, 5, 1, 12, 5, 5, 5, 10, 5, 5, 10, 5, 5, 5, 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, 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, 3, 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, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 6, 3, 3, 12, 17, 29, 29, 44, 44, 44, 44, 44, 44, 3, 2, 2, 2, 2, 3, 3, 3, 2, 1, 1, 1, 3, 3, 6, 6, 6, 17, 17, 29, 29, 29, 29, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 3, 2, 2, 4] 100 rigid atoms, others: [11, 4, 5, 38, 7, 8, 9, 10, 39, 40, 6] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 201) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/201 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/201' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2ccc(OC)c(OCCC[N@]3CC[N@@](C)CC3)c2)ccc1O) `ZINC001184255474.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184255474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184255474 none COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2ccc(OC)c(OCCC[N@]3CC[N@@](C)CC3)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', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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', '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, 5, 1, 12, 5, 5, 5, 10, 5, 5, 10, 5, 5, 5, 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, 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, 3, 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, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 6, 3, 3, 12, 17, 29, 29, 44, 44, 44, 44, 44, 44, 3, 2, 2, 2, 2, 3, 3, 3, 2, 1, 1, 1, 3, 3, 6, 6, 6, 17, 17, 29, 29, 29, 29, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 3, 2, 2, 4] 100 rigid atoms, others: [11, 4, 5, 38, 7, 8, 9, 10, 39, 40, 6] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 202) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/202 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/202' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2ccc(OC)c(OCCC[N@]3CC[N@](C)CC3)c2)ccc1O) `ZINC001184255474.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184255474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184255474 none COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2ccc(OC)c(OCCC[N@]3CC[N@](C)CC3)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', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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', '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, 5, 1, 12, 5, 5, 5, 10, 5, 5, 10, 5, 5, 5, 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, 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, 3, 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, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 6, 3, 3, 12, 16, 27, 27, 40, 40, 40, 40, 40, 40, 3, 2, 2, 2, 2, 3, 3, 3, 2, 1, 1, 1, 3, 3, 6, 6, 6, 16, 16, 27, 27, 27, 27, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 3, 2, 2, 4] 100 rigid atoms, others: [11, 4, 5, 38, 7, 8, 9, 10, 39, 40, 6] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 203) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/203 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/203' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2ccc(OC)c(OCCC[N@]3CC[N@@](C)CC3)c2)ccc1O) `ZINC001184255474.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184255474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184255474 none COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2ccc(OC)c(OCCC[N@]3CC[N@@](C)CC3)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', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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', '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, 5, 1, 12, 5, 5, 5, 10, 5, 5, 10, 5, 5, 5, 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, 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, 3, 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, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 6, 3, 3, 12, 17, 29, 29, 44, 44, 44, 44, 44, 44, 3, 2, 2, 2, 2, 3, 3, 3, 2, 1, 1, 1, 3, 3, 6, 6, 6, 17, 17, 29, 29, 29, 29, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 3, 2, 2, 4] 100 rigid atoms, others: [11, 4, 5, 38, 7, 8, 9, 10, 39, 40, 6] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184255474 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474 Building ZINC001184255474 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184255474 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 200) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/200: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2ccc(OC)c(OCCC[N@]3CC[N@](C)CC3)c2)ccc1O) `ZINC001184255474.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184255474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184255474 none COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2ccc(OC)c(OCCC[N@]3CC[N@](C)CC3)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', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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', '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, 5, 1, 12, 5, 5, 5, 10, 5, 5, 10, 5, 5, 5, 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, 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, 3, 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, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 6, 3, 3, 12, 17, 29, 29, 44, 44, 44, 44, 44, 44, 3, 2, 2, 2, 2, 3, 3, 3, 2, 1, 1, 1, 3, 3, 6, 6, 6, 17, 17, 29, 29, 29, 29, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 3, 2, 2, 4] 100 rigid atoms, others: [11, 4, 5, 38, 7, 8, 9, 10, 39, 40, 6] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 201) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/201: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2ccc(OC)c(OCCC[N@]3CC[N@@](C)CC3)c2)ccc1O) `ZINC001184255474.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184255474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184255474 none COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2ccc(OC)c(OCCC[N@]3CC[N@@](C)CC3)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', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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', '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, 5, 1, 12, 5, 5, 5, 10, 5, 5, 10, 5, 5, 5, 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, 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, 3, 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, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 6, 3, 3, 12, 17, 29, 29, 44, 44, 44, 44, 44, 44, 3, 2, 2, 2, 2, 3, 3, 3, 2, 1, 1, 1, 3, 3, 6, 6, 6, 17, 17, 29, 29, 29, 29, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 3, 2, 2, 4] 100 rigid atoms, others: [11, 4, 5, 38, 7, 8, 9, 10, 39, 40, 6] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 202) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/202: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(OC)c(OCCC[N@]3CC[N@](C)CC3)c2)ccc1O) `ZINC001184255474.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184255474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184255474 none COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2ccc(OC)c(OCCC[N@]3CC[N@](C)CC3)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', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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', '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, 5, 1, 12, 5, 5, 5, 10, 5, 5, 10, 5, 5, 5, 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, 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, 3, 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, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 6, 3, 3, 12, 16, 27, 27, 40, 40, 40, 40, 40, 40, 3, 2, 2, 2, 2, 3, 3, 3, 2, 1, 1, 1, 3, 3, 6, 6, 6, 16, 16, 27, 27, 27, 27, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 3, 2, 2, 4] 100 rigid atoms, others: [11, 4, 5, 38, 7, 8, 9, 10, 39, 40, 6] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 203) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/203: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(OC)c(OCCC[N@]3CC[N@@](C)CC3)c2)ccc1O) `ZINC001184255474.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184255474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184255474 none COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2ccc(OC)c(OCCC[N@]3CC[N@@](C)CC3)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', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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', '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, 5, 1, 12, 5, 5, 5, 10, 5, 5, 10, 5, 5, 5, 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, 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, 3, 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, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 6, 3, 3, 12, 17, 29, 29, 44, 44, 44, 44, 44, 44, 3, 2, 2, 2, 2, 3, 3, 3, 2, 1, 1, 1, 3, 3, 6, 6, 6, 17, 17, 29, 29, 29, 29, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 3, 2, 2, 4] 100 rigid atoms, others: [11, 4, 5, 38, 7, 8, 9, 10, 39, 40, 6] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184255474 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474 Building ZINC001184255474 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184255474 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 200) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/200: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2ccc(OC)c(OCCC[N@]3CC[N@](C)CC3)c2)ccc1O) `ZINC001184255474.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184255474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184255474 none COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2ccc(OC)c(OCCC[N@]3CC[N@](C)CC3)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', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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', '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, 5, 1, 12, 5, 5, 5, 10, 5, 5, 10, 5, 5, 5, 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, 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, 3, 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, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 6, 3, 3, 12, 17, 29, 29, 44, 44, 44, 44, 44, 44, 3, 2, 2, 2, 2, 3, 3, 3, 2, 1, 1, 1, 3, 3, 6, 6, 6, 17, 17, 29, 29, 29, 29, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 3, 2, 2, 4] 100 rigid atoms, others: [11, 4, 5, 38, 7, 8, 9, 10, 39, 40, 6] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 201) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/201: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2ccc(OC)c(OCCC[N@]3CC[N@@](C)CC3)c2)ccc1O) `ZINC001184255474.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184255474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184255474 none COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2ccc(OC)c(OCCC[N@]3CC[N@@](C)CC3)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', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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', '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, 5, 1, 12, 5, 5, 5, 10, 5, 5, 10, 5, 5, 5, 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, 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, 3, 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, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 6, 3, 3, 12, 17, 29, 29, 44, 44, 44, 44, 44, 44, 3, 2, 2, 2, 2, 3, 3, 3, 2, 1, 1, 1, 3, 3, 6, 6, 6, 17, 17, 29, 29, 29, 29, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 3, 2, 2, 4] 100 rigid atoms, others: [11, 4, 5, 38, 7, 8, 9, 10, 39, 40, 6] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 202) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/202: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(OC)c(OCCC[N@]3CC[N@](C)CC3)c2)ccc1O) `ZINC001184255474.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184255474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184255474 none COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2ccc(OC)c(OCCC[N@]3CC[N@](C)CC3)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', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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', '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, 5, 1, 12, 5, 5, 5, 10, 5, 5, 10, 5, 5, 5, 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, 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, 3, 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, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 6, 3, 3, 12, 16, 27, 27, 40, 40, 40, 40, 40, 40, 3, 2, 2, 2, 2, 3, 3, 3, 2, 1, 1, 1, 3, 3, 6, 6, 6, 16, 16, 27, 27, 27, 27, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 3, 2, 2, 4] 100 rigid atoms, others: [11, 4, 5, 38, 7, 8, 9, 10, 39, 40, 6] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 203) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/203: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(OC)c(OCCC[N@]3CC[N@@](C)CC3)c2)ccc1O) `ZINC001184255474.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184255474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184255474 none COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2ccc(OC)c(OCCC[N@]3CC[N@@](C)CC3)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', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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', '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, 5, 1, 12, 5, 5, 5, 10, 5, 5, 10, 5, 5, 5, 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, 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, 3, 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, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 6, 3, 3, 12, 17, 29, 29, 44, 44, 44, 44, 44, 44, 3, 2, 2, 2, 2, 3, 3, 3, 2, 1, 1, 1, 3, 3, 6, 6, 6, 17, 17, 29, 29, 29, 29, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 3, 2, 2, 4] 100 rigid atoms, others: [11, 4, 5, 38, 7, 8, 9, 10, 39, 40, 6] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184255474 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474 Building ZINC001184255474 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184255474 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 200) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/200: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2ccc(OC)c(OCCC[N@]3CC[N@](C)CC3)c2)ccc1O) `ZINC001184255474.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184255474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184255474 none COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2ccc(OC)c(OCCC[N@]3CC[N@](C)CC3)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', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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', '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, 5, 1, 12, 5, 5, 5, 10, 5, 5, 10, 5, 5, 5, 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, 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, 3, 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, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 6, 3, 3, 12, 17, 29, 29, 44, 44, 44, 44, 44, 44, 3, 2, 2, 2, 2, 3, 3, 3, 2, 1, 1, 1, 3, 3, 6, 6, 6, 17, 17, 29, 29, 29, 29, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 3, 2, 2, 4] 100 rigid atoms, others: [11, 4, 5, 38, 7, 8, 9, 10, 39, 40, 6] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 201) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/201: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2ccc(OC)c(OCCC[N@]3CC[N@@](C)CC3)c2)ccc1O) `ZINC001184255474.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184255474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184255474 none COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2ccc(OC)c(OCCC[N@]3CC[N@@](C)CC3)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', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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', '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, 5, 1, 12, 5, 5, 5, 10, 5, 5, 10, 5, 5, 5, 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, 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, 3, 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, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 6, 3, 3, 12, 17, 29, 29, 44, 44, 44, 44, 44, 44, 3, 2, 2, 2, 2, 3, 3, 3, 2, 1, 1, 1, 3, 3, 6, 6, 6, 17, 17, 29, 29, 29, 29, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 3, 2, 2, 4] 100 rigid atoms, others: [11, 4, 5, 38, 7, 8, 9, 10, 39, 40, 6] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 202) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/202: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(OC)c(OCCC[N@]3CC[N@](C)CC3)c2)ccc1O) `ZINC001184255474.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184255474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184255474 none COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2ccc(OC)c(OCCC[N@]3CC[N@](C)CC3)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', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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', '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, 5, 1, 12, 5, 5, 5, 10, 5, 5, 10, 5, 5, 5, 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, 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, 3, 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, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 6, 3, 3, 12, 16, 27, 27, 40, 40, 40, 40, 40, 40, 3, 2, 2, 2, 2, 3, 3, 3, 2, 1, 1, 1, 3, 3, 6, 6, 6, 16, 16, 27, 27, 27, 27, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 3, 2, 2, 4] 100 rigid atoms, others: [11, 4, 5, 38, 7, 8, 9, 10, 39, 40, 6] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 203) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/203: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(OC)c(OCCC[N@]3CC[N@@](C)CC3)c2)ccc1O) `ZINC001184255474.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184255474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184255474 none COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2ccc(OC)c(OCCC[N@]3CC[N@@](C)CC3)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', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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', '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, 5, 1, 12, 5, 5, 5, 10, 5, 5, 10, 5, 5, 5, 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, 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, 3, 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, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 6, 3, 3, 12, 17, 29, 29, 44, 44, 44, 44, 44, 44, 3, 2, 2, 2, 2, 3, 3, 3, 2, 1, 1, 1, 3, 3, 6, 6, 6, 17, 17, 29, 29, 29, 29, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 3, 2, 2, 4] 100 rigid atoms, others: [11, 4, 5, 38, 7, 8, 9, 10, 39, 40, 6] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184255474 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184255474 Building ZINC001184256399 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256399' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256399 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184256399 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256399/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256399 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 204) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/204 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/204' -> `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](CN)C(=O)OCC2c3ccccc3-c3ccccc32)ccc1O) `ZINC001184256399.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184256399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184256399 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N[C@H](CN)C(=O)OCC2c3ccccc3-c3ccccc32)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 10, 1, 11, 12, 5, 5, 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, 6, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 4, 4, 2, 1, 1, 1, 1, 2, 2, 2, 4, 4, 5, 4, 5, 5, 8, 24, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 4, 4, 4, 4, 8, 8, 8, 4, 2, 2, 2, 5, 5, 5, 5, 24, 24, 32, 32, 32, 32, 32, 32, 32, 32, 32, 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, 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/418326/xbt-8058088.46/working/building/ZINC001184256399 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256399/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256399 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 205) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/205 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/205' -> `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](CN)C(=O)OCC2c3ccccc3-c3ccccc32)ccc1O) `ZINC001184256399.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184256399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256399/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184256399 none COc1cc(C[C@]([O-])([SiH3])C(=O)N[C@H](CN)C(=O)OCC2c3ccccc3-c3ccccc32)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 10, 1, 11, 12, 5, 5, 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, 6, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 2, 4, 4, 7, 18, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 4, 4, 4, 4, 6, 6, 6, 4, 2, 2, 1, 3, 3, 3, 3, 18, 18, 29, 29, 29, 29, 29, 29, 29, 29, 29, 4, 4, 8] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 42] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 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/418326/xbt-8058088.46/working/building/ZINC001184256399 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184256399 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256399/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256399/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256399 Building ZINC001184256399 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256399' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256399 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184256399 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256399/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256399 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 204) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)N[C@H](CN)C(=O)OCC2c3ccccc3-c3ccccc32)ccc1O) `ZINC001184256399.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184256399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184256399 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N[C@H](CN)C(=O)OCC2c3ccccc3-c3ccccc32)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 10, 1, 11, 12, 5, 5, 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, 6, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 4, 4, 2, 1, 1, 1, 1, 2, 2, 2, 4, 4, 5, 4, 5, 5, 8, 24, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 4, 4, 4, 4, 8, 8, 8, 4, 2, 2, 2, 5, 5, 5, 5, 24, 24, 32, 32, 32, 32, 32, 32, 32, 32, 32, 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, 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/418326/xbt-8058088.46/working/building/ZINC001184256399 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256399/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256399 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 205) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N[C@H](CN)C(=O)OCC2c3ccccc3-c3ccccc32)ccc1O) `ZINC001184256399.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184256399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256399/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184256399 none COc1cc(C[C@]([O-])([SiH3])C(=O)N[C@H](CN)C(=O)OCC2c3ccccc3-c3ccccc32)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 10, 1, 11, 12, 5, 5, 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, 6, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 2, 4, 4, 7, 18, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 4, 4, 4, 4, 6, 6, 6, 4, 2, 2, 1, 3, 3, 3, 3, 18, 18, 29, 29, 29, 29, 29, 29, 29, 29, 29, 4, 4, 8] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 42] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 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/418326/xbt-8058088.46/working/building/ZINC001184256399 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184256399 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256399/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256399/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256399 Building ZINC001184256401 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256401' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256401 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184256401 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256401/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256401 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 206) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/206 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/206' -> `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](CN)C(=O)OCC2c3ccccc3-c3ccccc32)ccc1O) `ZINC001184256401.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184256401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184256401 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N[C@@H](CN)C(=O)OCC2c3ccccc3-c3ccccc32)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 10, 1, 11, 12, 5, 5, 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, 6, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 19, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4, 4, 7, 7, 7, 4, 2, 2, 1, 1, 1, 1, 1, 19, 19, 28, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 8] 100 rigid atoms, others: [45, 43, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 44, 46, 42] set([0, 1, 2, 3, 4, 16, 17, 18, 19, 20, 21, 22, 23, 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, 57, 58, 59, 60]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256401 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256401/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256401 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 207) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/207 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/207' -> `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](CN)C(=O)OCC2c3ccccc3-c3ccccc32)ccc1O) `ZINC001184256401.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184256401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256401/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184256401 none COc1cc(C[C@]([O-])([SiH3])C(=O)N[C@@H](CN)C(=O)OCC2c3ccccc3-c3ccccc32)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 10, 1, 11, 12, 5, 5, 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, 6, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [9, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 4, 4, 8, 20, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 4, 4, 4, 4, 9, 9, 9, 4, 2, 2, 1, 2, 2, 2, 2, 20, 20, 31, 31, 31, 31, 31, 31, 31, 31, 31, 4, 4, 8] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 42] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 137 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256401 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184256401 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256401/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256401/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256401 Building ZINC001184256401 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256401' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256401 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184256401 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256401/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256401 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 206) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)N[C@@H](CN)C(=O)OCC2c3ccccc3-c3ccccc32)ccc1O) `ZINC001184256401.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184256401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184256401 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N[C@@H](CN)C(=O)OCC2c3ccccc3-c3ccccc32)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 10, 1, 11, 12, 5, 5, 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, 6, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 19, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4, 4, 7, 7, 7, 4, 2, 2, 1, 1, 1, 1, 1, 19, 19, 28, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 8] 100 rigid atoms, others: [45, 43, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 44, 46, 42] set([0, 1, 2, 3, 4, 16, 17, 18, 19, 20, 21, 22, 23, 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, 57, 58, 59, 60]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256401 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256401/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256401 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 207) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N[C@@H](CN)C(=O)OCC2c3ccccc3-c3ccccc32)ccc1O) `ZINC001184256401.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184256401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256401/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184256401 none COc1cc(C[C@]([O-])([SiH3])C(=O)N[C@@H](CN)C(=O)OCC2c3ccccc3-c3ccccc32)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 10, 1, 11, 12, 5, 5, 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, 6, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [9, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 4, 4, 8, 20, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 4, 4, 4, 4, 9, 9, 9, 4, 2, 2, 1, 2, 2, 2, 2, 20, 20, 31, 31, 31, 31, 31, 31, 31, 31, 31, 4, 4, 8] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 42] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 137 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256401 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184256401 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256401/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256401/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256401 Building ZINC001184256566 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256566' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256566 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184256566 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256566/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256566 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 208) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/208 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/208' -> `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]2CCc3ccccc3N(CC(=O)OC(C)(C)C)C2=O)ccc1O) `ZINC001184256566.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184256566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184256566 none COc1cc(C[C@]([O-])([SiH3])C(=O)N[C@H]2CCc3ccccc3N(CC(=O)OC(C)(C)C)C2=O)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 12, 5, 5, 5, 5, 1, 11, 1, 1, 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, 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, 5, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 5, 5, 5, 3, 1, 1, 1, 1, 2, 2, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 17, 32, 32, 32, 32, 32, 32, 7, 7, 5, 5, 5, 5, 12, 12, 12, 5, 3, 3, 2, 7, 7, 7, 7, 7, 7, 7, 7, 17, 17, 32, 32, 32, 32, 32, 32, 32, 32, 32, 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, 60, 61, 62, 63, 64]) total number of confs: 150 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256566 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256566/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256566 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 209) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/209 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/209' -> `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]2CCc3ccccc3N(CC(=O)OC(C)(C)C)C2=O)ccc1O) `ZINC001184256566.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184256566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256566/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184256566 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N[C@H]2CCc3ccccc3N(CC(=O)OC(C)(C)C)C2=O)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 12, 5, 5, 5, 5, 1, 11, 1, 1, 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, 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, 5, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 17, 23, 23, 27, 27, 27, 27, 7, 7, 4, 4, 4, 4, 11, 11, 11, 4, 2, 2, 1, 7, 7, 7, 7, 7, 7, 7, 7, 17, 17, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 4, 8] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 42] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 124 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256566 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184256566 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256566/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256566/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256566 Building ZINC001184256566 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256566' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256566 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184256566 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256566/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256566 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 208) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)N[C@H]2CCc3ccccc3N(CC(=O)OC(C)(C)C)C2=O)ccc1O) `ZINC001184256566.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184256566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184256566 none COc1cc(C[C@]([O-])([SiH3])C(=O)N[C@H]2CCc3ccccc3N(CC(=O)OC(C)(C)C)C2=O)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 12, 5, 5, 5, 5, 1, 11, 1, 1, 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, 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, 5, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 5, 5, 5, 3, 1, 1, 1, 1, 2, 2, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 17, 32, 32, 32, 32, 32, 32, 7, 7, 5, 5, 5, 5, 12, 12, 12, 5, 3, 3, 2, 7, 7, 7, 7, 7, 7, 7, 7, 17, 17, 32, 32, 32, 32, 32, 32, 32, 32, 32, 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, 60, 61, 62, 63, 64]) total number of confs: 150 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256566 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256566/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256566 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 209) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)N[C@H]2CCc3ccccc3N(CC(=O)OC(C)(C)C)C2=O)ccc1O) `ZINC001184256566.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184256566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256566/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184256566 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N[C@H]2CCc3ccccc3N(CC(=O)OC(C)(C)C)C2=O)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 12, 5, 5, 5, 5, 1, 11, 1, 1, 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, 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, 5, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 17, 23, 23, 27, 27, 27, 27, 7, 7, 4, 4, 4, 4, 11, 11, 11, 4, 2, 2, 1, 7, 7, 7, 7, 7, 7, 7, 7, 17, 17, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 4, 8] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 42] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 124 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256566 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184256566 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256566/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256566/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184256566 Building ZINC001184317388 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317388' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317388 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184317388 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317388/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317388 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 210) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/210 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/210' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1ncnc2c1ncn2CCOC[P@](=O)(O)OCOC(=O)C(C)(C)C) `ZINC001184317388.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184317388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184317388 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1ncnc2c1ncn2CCOC[P@](=O)(O)OCOC(=O)C(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', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'P.3', 'O.2', 'O.3', 'O.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 5, 5, 12, 5, 13, 11, 12, 12, 5, 12, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 5, 4, 3, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 8, 13, 17, 27, 27, 27, 34, 44, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 7, 7, 8, 8, 17, 17, 27, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317388 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317388/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317388 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 211) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/211 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/211' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1ncnc2c1ncn2CCOC[P@](=O)(O)OCOC(=O)C(C)(C)C) `ZINC001184317388.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184317388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317388/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184317388 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1ncnc2c1ncn2CCOC[P@](=O)(O)OCOC(=O)C(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', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'P.3', 'O.2', 'O.3', 'O.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 5, 5, 12, 5, 13, 11, 12, 12, 5, 12, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 5, 4, 3, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 10, 13, 16, 26, 26, 26, 35, 47, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 8, 8, 10, 10, 16, 16, 26, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 41, 42, 7, 3, 4, 6, 5] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 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: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317388 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184317388 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317388/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317388/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317388 Building ZINC001184317388 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317388' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317388 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184317388 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317388/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317388 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 210) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/210: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1ncnc2c1ncn2CCOC[P@](=O)(O)OCOC(=O)C(C)(C)C) `ZINC001184317388.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184317388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184317388 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1ncnc2c1ncn2CCOC[P@](=O)(O)OCOC(=O)C(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', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'P.3', 'O.2', 'O.3', 'O.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 5, 5, 12, 5, 13, 11, 12, 12, 5, 12, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 5, 4, 3, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 8, 13, 17, 27, 27, 27, 34, 44, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 7, 7, 8, 8, 17, 17, 27, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317388 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317388/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317388 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 211) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/211: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1ncnc2c1ncn2CCOC[P@](=O)(O)OCOC(=O)C(C)(C)C) `ZINC001184317388.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184317388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317388/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184317388 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1ncnc2c1ncn2CCOC[P@](=O)(O)OCOC(=O)C(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', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'P.3', 'O.2', 'O.3', 'O.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 5, 5, 12, 5, 13, 11, 12, 12, 5, 12, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 5, 4, 3, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 10, 13, 16, 26, 26, 26, 35, 47, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 8, 8, 10, 10, 16, 16, 26, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 41, 42, 7, 3, 4, 6, 5] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 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: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317388 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184317388 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317388/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317388/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317388 Building ZINC001184317389 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317389' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317389 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184317389 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317389/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317389 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 212) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/212 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/212' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1ncnc2c1ncn2CCOC[P@](=O)(O)OCOC(=O)C(C)(C)C) `ZINC001184317389.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184317389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184317389 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1ncnc2c1ncn2CCOC[P@](=O)(O)OCOC(=O)C(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', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'P.3', 'O.2', 'O.3', 'O.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 5, 5, 12, 5, 13, 11, 12, 12, 5, 12, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 5, 4, 3, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 9, 14, 18, 29, 29, 29, 35, 45, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 8, 8, 9, 9, 18, 18, 29, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317389 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317389/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317389 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 213) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/213 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/213' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1ncnc2c1ncn2CCOC[P@](=O)(O)OCOC(=O)C(C)(C)C) `ZINC001184317389.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184317389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317389/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184317389 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1ncnc2c1ncn2CCOC[P@](=O)(O)OCOC(=O)C(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', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'P.3', 'O.2', 'O.3', 'O.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 5, 5, 12, 5, 13, 11, 12, 12, 5, 12, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 5, 4, 3, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 9, 12, 15, 23, 23, 23, 32, 45, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 7, 7, 9, 9, 15, 15, 23, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 41, 42, 7, 3, 4, 6, 5] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 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: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317389 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184317389 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317389/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317389/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317389 Building ZINC001184317389 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317389' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317389 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184317389 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317389/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317389 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 212) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/212: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1ncnc2c1ncn2CCOC[P@](=O)(O)OCOC(=O)C(C)(C)C) `ZINC001184317389.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184317389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184317389 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1ncnc2c1ncn2CCOC[P@](=O)(O)OCOC(=O)C(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', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'P.3', 'O.2', 'O.3', 'O.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 5, 5, 12, 5, 13, 11, 12, 12, 5, 12, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 5, 4, 3, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 9, 14, 18, 29, 29, 29, 35, 45, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 8, 8, 9, 9, 18, 18, 29, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317389 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317389/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317389 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 213) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/213: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1ncnc2c1ncn2CCOC[P@](=O)(O)OCOC(=O)C(C)(C)C) `ZINC001184317389.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184317389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317389/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184317389 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1ncnc2c1ncn2CCOC[P@](=O)(O)OCOC(=O)C(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', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'P.3', 'O.2', 'O.3', 'O.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 5, 5, 12, 5, 13, 11, 12, 12, 5, 12, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 5, 4, 3, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 9, 12, 15, 23, 23, 23, 32, 45, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 7, 7, 9, 9, 15, 15, 23, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 41, 42, 7, 3, 4, 6, 5] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 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: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317389 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184317389 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317389/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317389/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317389 Building ZINC001184317599 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317599' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317599 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184317599 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317599/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317599 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 214) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/214 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/214' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1nonc1c1noc(=O)n1c1ccc(F)c(Br)c1) `ZINC001184317599.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184317599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317599/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001184317599 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1nonc1c1noc(=O)n1c1ccc(F)c(Br)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.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', '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, 12, 8, 1, 1, 8, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 8, 8, 8, 8, 8, 23, 23, 23, 23, 21, 23, 45, 45, 45, 45, 45, 45, 45, 3, 3, 3, 3, 3, 3, 3, 3, 3, 45, 45, 45] 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]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317599 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317599/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317599 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 215) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/215 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/215' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1nonc1c1noc(=O)n1c1ccc(F)c(Br)c1) `ZINC001184317599.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184317599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317599/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001184317599 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1nonc1c1noc(=O)n1c1ccc(F)c(Br)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.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', '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, 12, 8, 1, 1, 8, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 11, 11, 11, 11, 11, 26, 26, 26, 26, 24, 26, 47, 47, 47, 47, 47, 47, 47, 3, 3, 3, 3, 3, 3, 3, 3, 3, 47, 47, 47] 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317599 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184317599 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317599/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317599/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317599 Building ZINC001184317599 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317599' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317599 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184317599 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317599/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317599 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 214) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/214: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1nonc1c1noc(=O)n1c1ccc(F)c(Br)c1) `ZINC001184317599.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184317599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317599/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001184317599 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1nonc1c1noc(=O)n1c1ccc(F)c(Br)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.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', '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, 12, 8, 1, 1, 8, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 8, 8, 8, 8, 8, 23, 23, 23, 23, 21, 23, 45, 45, 45, 45, 45, 45, 45, 3, 3, 3, 3, 3, 3, 3, 3, 3, 45, 45, 45] 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]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317599 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317599/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317599 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 215) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/215: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1nonc1c1noc(=O)n1c1ccc(F)c(Br)c1) `ZINC001184317599.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184317599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317599/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001184317599 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1nonc1c1noc(=O)n1c1ccc(F)c(Br)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.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', '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, 12, 8, 1, 1, 8, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 11, 11, 11, 11, 11, 26, 26, 26, 26, 24, 26, 47, 47, 47, 47, 47, 47, 47, 3, 3, 3, 3, 3, 3, 3, 3, 3, 47, 47, 47] 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317599 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184317599 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317599/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317599/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317599 Building ZINC001184317600 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317600' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317600 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184317600 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317600/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317600 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 216) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/216 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/216' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1nonc1c1noc(=O)n1c1ccc(F)c(Br)c1) `ZINC001184317600.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184317600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001184317600 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1nonc1c1noc(=O)n1c1ccc(F)c(Br)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.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', '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, 12, 8, 1, 1, 8, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 10, 10, 10, 10, 10, 26, 26, 26, 26, 23, 26, 47, 47, 47, 47, 47, 47, 47, 3, 3, 3, 3, 3, 3, 3, 3, 3, 47, 47, 47] 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]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317600 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317600/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317600 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 217) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/217 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/217' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1nonc1c1noc(=O)n1c1ccc(F)c(Br)c1) `ZINC001184317600.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184317600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317600/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001184317600 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1nonc1c1noc(=O)n1c1ccc(F)c(Br)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.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', '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, 12, 8, 1, 1, 8, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 8, 8, 8, 8, 8, 23, 23, 23, 23, 21, 23, 45, 45, 45, 45, 45, 45, 45, 3, 3, 3, 3, 3, 3, 3, 3, 3, 45, 45, 45] 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]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317600 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184317600 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317600/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317600/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317600 Building ZINC001184317600 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317600' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317600 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184317600 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317600/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317600 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 216) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/216: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1nonc1c1noc(=O)n1c1ccc(F)c(Br)c1) `ZINC001184317600.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184317600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001184317600 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1nonc1c1noc(=O)n1c1ccc(F)c(Br)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.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', '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, 12, 8, 1, 1, 8, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 10, 10, 10, 10, 10, 26, 26, 26, 26, 23, 26, 47, 47, 47, 47, 47, 47, 47, 3, 3, 3, 3, 3, 3, 3, 3, 3, 47, 47, 47] 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]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317600 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317600/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317600 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 217) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/217: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1nonc1c1noc(=O)n1c1ccc(F)c(Br)c1) `ZINC001184317600.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184317600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317600/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001184317600 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1nonc1c1noc(=O)n1c1ccc(F)c(Br)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.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', '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, 12, 8, 1, 1, 8, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 8, 8, 8, 8, 8, 23, 23, 23, 23, 21, 23, 45, 45, 45, 45, 45, 45, 45, 3, 3, 3, 3, 3, 3, 3, 3, 3, 45, 45, 45] 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]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317600 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184317600 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317600/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317600/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184317600 Building ZINC001184318670 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318670' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318670 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184318670 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318670/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318670 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 218) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/218 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/218' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)O[C@H]2c3nccnc3C(=O)N2c2ccc(Cl)cn2)CC1) `ZINC001184318670.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184318670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318670/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184318670 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)O[C@H]2c3nccnc3C(=O)N2c2ccc(Cl)cn2)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', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 7, 1, 8, 1, 1, 8, 1, 1, 11, 8, 1, 1, 1, 1, 16, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 8, 17, 23, 23, 23, 23, 34, 34, 45, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 48, 48, 48, 48, 48, 48, 23, 23, 3, 3, 3, 3, 3, 3, 3, 3, 23, 23, 23, 23, 47, 47, 48, 48, 48, 23, 23, 23, 23] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 119 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318670 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318670/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318670 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 219) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/219 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/219' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)O[C@H]2c3nccnc3C(=O)N2c2ccc(Cl)cn2)CC1) `ZINC001184318670.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184318670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318670/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184318670 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)O[C@H]2c3nccnc3C(=O)N2c2ccc(Cl)cn2)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', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 7, 1, 8, 1, 1, 8, 1, 1, 11, 8, 1, 1, 1, 1, 16, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 7, 17, 24, 24, 24, 24, 34, 34, 47, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 50, 50, 50, 50, 50, 50, 24, 24, 2, 2, 2, 2, 2, 2, 2, 2, 24, 24, 24, 24, 48, 48, 50, 50, 50, 24, 24, 24, 24] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 115 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318670 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184318670 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318670/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318670/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318670 Building ZINC001184318670 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318670' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318670 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184318670 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318670/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318670 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 218) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/218: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)O[C@H]2c3nccnc3C(=O)N2c2ccc(Cl)cn2)CC1) `ZINC001184318670.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184318670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318670/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184318670 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)O[C@H]2c3nccnc3C(=O)N2c2ccc(Cl)cn2)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', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 7, 1, 8, 1, 1, 8, 1, 1, 11, 8, 1, 1, 1, 1, 16, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 8, 17, 23, 23, 23, 23, 34, 34, 45, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 48, 48, 48, 48, 48, 48, 23, 23, 3, 3, 3, 3, 3, 3, 3, 3, 23, 23, 23, 23, 47, 47, 48, 48, 48, 23, 23, 23, 23] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 119 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318670 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318670/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318670 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 219) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/219: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)O[C@H]2c3nccnc3C(=O)N2c2ccc(Cl)cn2)CC1) `ZINC001184318670.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184318670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318670/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184318670 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)O[C@H]2c3nccnc3C(=O)N2c2ccc(Cl)cn2)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', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 7, 1, 8, 1, 1, 8, 1, 1, 11, 8, 1, 1, 1, 1, 16, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 7, 17, 24, 24, 24, 24, 34, 34, 47, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 50, 50, 50, 50, 50, 50, 24, 24, 2, 2, 2, 2, 2, 2, 2, 2, 24, 24, 24, 24, 48, 48, 50, 50, 50, 24, 24, 24, 24] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 115 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318670 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184318670 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318670/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318670/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318670 Building ZINC001184318671 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318671' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318671 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184318671 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318671/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318671 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 220) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/220 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/220' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)O[C@@H]2c3nccnc3C(=O)N2c2ccc(Cl)cn2)CC1) `ZINC001184318671.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184318671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318671/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184318671 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)O[C@@H]2c3nccnc3C(=O)N2c2ccc(Cl)cn2)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', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 7, 1, 8, 1, 1, 8, 1, 1, 11, 8, 1, 1, 1, 1, 16, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 9, 18, 23, 23, 23, 23, 35, 35, 45, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 23, 23, 3, 3, 3, 3, 3, 3, 3, 3, 23, 23, 23, 23, 48, 48, 48, 48, 48, 23, 23, 23, 23] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 126 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318671 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318671/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318671 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 221) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/221 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/221' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)O[C@@H]2c3nccnc3C(=O)N2c2ccc(Cl)cn2)CC1) `ZINC001184318671.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184318671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318671/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184318671 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)O[C@@H]2c3nccnc3C(=O)N2c2ccc(Cl)cn2)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', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 7, 1, 8, 1, 1, 8, 1, 1, 11, 8, 1, 1, 1, 1, 16, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 7, 17, 23, 23, 23, 23, 31, 31, 44, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 48, 48, 48, 48, 48, 48, 23, 23, 3, 3, 3, 3, 3, 3, 3, 3, 23, 23, 23, 23, 45, 45, 48, 48, 48, 23, 23, 23, 23] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 112 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318671 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184318671 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318671/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318671/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318671 Building ZINC001184318671 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318671' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318671 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184318671 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318671/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318671 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 220) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/220: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)O[C@@H]2c3nccnc3C(=O)N2c2ccc(Cl)cn2)CC1) `ZINC001184318671.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184318671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318671/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184318671 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)O[C@@H]2c3nccnc3C(=O)N2c2ccc(Cl)cn2)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', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 7, 1, 8, 1, 1, 8, 1, 1, 11, 8, 1, 1, 1, 1, 16, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 9, 18, 23, 23, 23, 23, 35, 35, 45, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 23, 23, 3, 3, 3, 3, 3, 3, 3, 3, 23, 23, 23, 23, 48, 48, 48, 48, 48, 23, 23, 23, 23] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 126 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318671 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318671/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318671 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 221) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/221: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)O[C@@H]2c3nccnc3C(=O)N2c2ccc(Cl)cn2)CC1) `ZINC001184318671.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184318671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318671/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184318671 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)O[C@@H]2c3nccnc3C(=O)N2c2ccc(Cl)cn2)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', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 7, 1, 8, 1, 1, 8, 1, 1, 11, 8, 1, 1, 1, 1, 16, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 7, 17, 23, 23, 23, 23, 31, 31, 44, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 48, 48, 48, 48, 48, 48, 23, 23, 3, 3, 3, 3, 3, 3, 3, 3, 23, 23, 23, 23, 45, 45, 48, 48, 48, 23, 23, 23, 23] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 112 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318671 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184318671 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318671/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318671/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318671 Building ZINC001184318672 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318672' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318672 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184318672 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318672/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318672 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 222) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/222 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/222' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)O[C@@H]2c3nccnc3C(=O)N2c2ccc(Cl)cn2)CC1) `ZINC001184318672.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184318672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184318672 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)O[C@@H]2c3nccnc3C(=O)N2c2ccc(Cl)cn2)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', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 7, 1, 8, 1, 1, 8, 1, 1, 11, 8, 1, 1, 1, 1, 16, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 9, 17, 23, 23, 23, 23, 35, 35, 45, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 23, 23, 3, 3, 3, 3, 3, 3, 3, 3, 23, 23, 23, 23, 48, 48, 48, 48, 48, 23, 23, 23, 23] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 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: 127 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318672 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318672/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318672 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 223) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/223 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/223' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)O[C@@H]2c3nccnc3C(=O)N2c2ccc(Cl)cn2)CC1) `ZINC001184318672.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184318672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318672/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184318672 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)O[C@@H]2c3nccnc3C(=O)N2c2ccc(Cl)cn2)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', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 7, 1, 8, 1, 1, 8, 1, 1, 11, 8, 1, 1, 1, 1, 16, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 7, 17, 22, 22, 22, 22, 32, 32, 46, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 49, 49, 49, 49, 49, 49, 22, 22, 3, 3, 3, 3, 3, 3, 3, 3, 22, 22, 22, 22, 47, 47, 49, 49, 49, 22, 22, 22, 22] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 117 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318672 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184318672 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318672/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318672/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318672 Building ZINC001184318672 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318672' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318672 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184318672 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318672/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318672 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 222) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/222: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)O[C@@H]2c3nccnc3C(=O)N2c2ccc(Cl)cn2)CC1) `ZINC001184318672.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184318672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184318672 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)O[C@@H]2c3nccnc3C(=O)N2c2ccc(Cl)cn2)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', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 7, 1, 8, 1, 1, 8, 1, 1, 11, 8, 1, 1, 1, 1, 16, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 9, 17, 23, 23, 23, 23, 35, 35, 45, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 23, 23, 3, 3, 3, 3, 3, 3, 3, 3, 23, 23, 23, 23, 48, 48, 48, 48, 48, 23, 23, 23, 23] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 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: 127 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318672 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318672/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318672 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 223) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/223: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)O[C@@H]2c3nccnc3C(=O)N2c2ccc(Cl)cn2)CC1) `ZINC001184318672.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184318672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318672/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184318672 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)O[C@@H]2c3nccnc3C(=O)N2c2ccc(Cl)cn2)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', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 7, 1, 8, 1, 1, 8, 1, 1, 11, 8, 1, 1, 1, 1, 16, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 7, 17, 22, 22, 22, 22, 32, 32, 46, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 49, 49, 49, 49, 49, 49, 22, 22, 3, 3, 3, 3, 3, 3, 3, 3, 22, 22, 22, 22, 47, 47, 49, 49, 49, 22, 22, 22, 22] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 117 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318672 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184318672 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318672/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318672/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318672 Building ZINC001184318673 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318673' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318673 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184318673 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318673/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318673 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 224) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/224 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/224' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)O[C@H]2c3nccnc3C(=O)N2c2ccc(Cl)cn2)CC1) `ZINC001184318673.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184318673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184318673 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)O[C@H]2c3nccnc3C(=O)N2c2ccc(Cl)cn2)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', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 7, 1, 8, 1, 1, 8, 1, 1, 11, 8, 1, 1, 1, 1, 16, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 8, 18, 24, 24, 24, 24, 34, 34, 45, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 48, 48, 48, 48, 48, 48, 24, 24, 3, 3, 3, 3, 3, 3, 3, 3, 24, 24, 24, 24, 46, 46, 48, 48, 48, 24, 24, 24, 24] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 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: 113 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318673 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318673/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318673 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 225) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/225 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/225' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)O[C@H]2c3nccnc3C(=O)N2c2ccc(Cl)cn2)CC1) `ZINC001184318673.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184318673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318673/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184318673 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)O[C@H]2c3nccnc3C(=O)N2c2ccc(Cl)cn2)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', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 7, 1, 8, 1, 1, 8, 1, 1, 11, 8, 1, 1, 1, 1, 16, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 7, 17, 24, 24, 24, 24, 33, 33, 47, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 50, 50, 50, 50, 50, 50, 24, 24, 2, 2, 2, 2, 2, 2, 2, 2, 24, 24, 24, 24, 48, 48, 50, 50, 50, 24, 24, 24, 24] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 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: 113 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318673 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184318673 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318673/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318673/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318673 Building ZINC001184318673 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318673' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318673 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184318673 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318673/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318673 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 224) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)O[C@H]2c3nccnc3C(=O)N2c2ccc(Cl)cn2)CC1) `ZINC001184318673.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184318673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184318673 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)O[C@H]2c3nccnc3C(=O)N2c2ccc(Cl)cn2)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', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 7, 1, 8, 1, 1, 8, 1, 1, 11, 8, 1, 1, 1, 1, 16, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 8, 18, 24, 24, 24, 24, 34, 34, 45, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 48, 48, 48, 48, 48, 48, 24, 24, 3, 3, 3, 3, 3, 3, 3, 3, 24, 24, 24, 24, 46, 46, 48, 48, 48, 24, 24, 24, 24] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 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: 113 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318673 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318673/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318673 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 225) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC[C@H](C)[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)O[C@H]2c3nccnc3C(=O)N2c2ccc(Cl)cn2)CC1) `ZINC001184318673.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184318673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318673/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184318673 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)O[C@H]2c3nccnc3C(=O)N2c2ccc(Cl)cn2)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', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 7, 1, 8, 1, 1, 8, 1, 1, 11, 8, 1, 1, 1, 1, 16, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 7, 17, 24, 24, 24, 24, 33, 33, 47, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 50, 50, 50, 50, 50, 50, 24, 24, 2, 2, 2, 2, 2, 2, 2, 2, 24, 24, 24, 24, 48, 48, 50, 50, 50, 24, 24, 24, 24] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 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: 113 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318673 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184318673 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318673/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318673/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184318673 Building ZINC001184322760 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184322760 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 226) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/226 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/226' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322760.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184322760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322760 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 7, 11, 7, 7, 16, 16, 16, 41, 47, 47, 47, 47, 47, 47, 47, 7, 7, 7, 7, 7, 7, 11, 2, 2, 2, 2, 2, 2, 2, 2, 3, 7, 11, 11, 11, 16, 41, 41, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 7, 11, 11, 11, 11, 11] 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]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 227) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/227 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/227' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322760.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184322760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322760 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 5, 5, 5, 10, 5, 5, 15, 14, 14, 42, 47, 47, 47, 47, 47, 47, 47, 5, 5, 5, 5, 5, 5, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 10, 10, 10, 15, 42, 42, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 5, 9, 9, 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, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 228) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/228 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/228' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322760.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184322760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322760 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 7, 11, 7, 7, 16, 16, 16, 41, 47, 47, 47, 47, 47, 47, 47, 7, 7, 7, 7, 7, 7, 11, 2, 2, 2, 2, 2, 2, 2, 2, 3, 7, 11, 11, 11, 16, 41, 41, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 7, 11, 11, 11, 11, 11] 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]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 229) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/229 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/229' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322760.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184322760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322760 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 5, 5, 5, 10, 5, 5, 15, 14, 14, 42, 47, 47, 47, 47, 47, 47, 47, 5, 5, 5, 5, 5, 5, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 10, 10, 10, 15, 42, 42, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 5, 9, 9, 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, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184322760 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760 Building ZINC001184322760 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184322760 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 226) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/226: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322760.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184322760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322760 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 7, 11, 7, 7, 16, 16, 16, 41, 47, 47, 47, 47, 47, 47, 47, 7, 7, 7, 7, 7, 7, 11, 2, 2, 2, 2, 2, 2, 2, 2, 3, 7, 11, 11, 11, 16, 41, 41, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 7, 11, 11, 11, 11, 11] 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]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 227) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/227: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322760.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184322760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322760 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 5, 5, 5, 10, 5, 5, 15, 14, 14, 42, 47, 47, 47, 47, 47, 47, 47, 5, 5, 5, 5, 5, 5, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 10, 10, 10, 15, 42, 42, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 5, 9, 9, 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, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 228) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/228: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322760.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184322760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322760 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 7, 11, 7, 7, 16, 16, 16, 41, 47, 47, 47, 47, 47, 47, 47, 7, 7, 7, 7, 7, 7, 11, 2, 2, 2, 2, 2, 2, 2, 2, 3, 7, 11, 11, 11, 16, 41, 41, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 7, 11, 11, 11, 11, 11] 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]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 229) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/229: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322760.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184322760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322760 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 5, 5, 5, 10, 5, 5, 15, 14, 14, 42, 47, 47, 47, 47, 47, 47, 47, 5, 5, 5, 5, 5, 5, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 10, 10, 10, 15, 42, 42, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 5, 9, 9, 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, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184322760 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760 Building ZINC001184322760 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184322760 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 226) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/226: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322760.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184322760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322760 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 7, 11, 7, 7, 16, 16, 16, 41, 47, 47, 47, 47, 47, 47, 47, 7, 7, 7, 7, 7, 7, 11, 2, 2, 2, 2, 2, 2, 2, 2, 3, 7, 11, 11, 11, 16, 41, 41, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 7, 11, 11, 11, 11, 11] 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]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 227) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/227: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322760.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184322760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322760 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 5, 5, 5, 10, 5, 5, 15, 14, 14, 42, 47, 47, 47, 47, 47, 47, 47, 5, 5, 5, 5, 5, 5, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 10, 10, 10, 15, 42, 42, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 5, 9, 9, 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, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 228) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/228: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322760.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184322760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322760 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 7, 11, 7, 7, 16, 16, 16, 41, 47, 47, 47, 47, 47, 47, 47, 7, 7, 7, 7, 7, 7, 11, 2, 2, 2, 2, 2, 2, 2, 2, 3, 7, 11, 11, 11, 16, 41, 41, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 7, 11, 11, 11, 11, 11] 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]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 229) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/229: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322760.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184322760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322760 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 5, 5, 5, 10, 5, 5, 15, 14, 14, 42, 47, 47, 47, 47, 47, 47, 47, 5, 5, 5, 5, 5, 5, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 10, 10, 10, 15, 42, 42, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 5, 9, 9, 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, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184322760 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760 Building ZINC001184322760 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184322760 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 226) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/226: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322760.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184322760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322760 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 7, 11, 7, 7, 16, 16, 16, 41, 47, 47, 47, 47, 47, 47, 47, 7, 7, 7, 7, 7, 7, 11, 2, 2, 2, 2, 2, 2, 2, 2, 3, 7, 11, 11, 11, 16, 41, 41, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 7, 11, 11, 11, 11, 11] 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]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 227) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/227: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322760.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184322760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322760 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 5, 5, 5, 10, 5, 5, 15, 14, 14, 42, 47, 47, 47, 47, 47, 47, 47, 5, 5, 5, 5, 5, 5, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 10, 10, 10, 15, 42, 42, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 5, 9, 9, 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, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 228) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/228: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322760.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184322760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322760 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 7, 11, 7, 7, 16, 16, 16, 41, 47, 47, 47, 47, 47, 47, 47, 7, 7, 7, 7, 7, 7, 11, 2, 2, 2, 2, 2, 2, 2, 2, 3, 7, 11, 11, 11, 16, 41, 41, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 7, 11, 11, 11, 11, 11] 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]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 229) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/229: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322760.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184322760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322760 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 5, 5, 5, 10, 5, 5, 15, 14, 14, 42, 47, 47, 47, 47, 47, 47, 47, 5, 5, 5, 5, 5, 5, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 10, 10, 10, 15, 42, 42, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 5, 9, 9, 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, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184322760 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322760 Building ZINC001184322762 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184322762 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 230) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/230 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/230' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322762.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184322762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322762 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 6, 10, 6, 6, 17, 16, 16, 41, 46, 46, 46, 46, 46, 46, 46, 6, 6, 6, 6, 6, 6, 9, 2, 2, 2, 2, 2, 2, 2, 2, 3, 6, 10, 10, 10, 17, 41, 41, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 6, 9, 9, 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, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 231) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/231 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/231' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322762.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184322762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322762 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 3, 6, 6, 6, 13, 6, 6, 15, 14, 14, 40, 46, 46, 46, 46, 46, 46, 46, 6, 6, 6, 6, 6, 6, 12, 4, 4, 4, 4, 4, 4, 4, 4, 3, 6, 13, 13, 13, 15, 40, 40, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 6, 12, 12, 12, 12, 12] 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]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 232) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/232 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/232' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322762.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184322762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322762 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 6, 10, 6, 6, 17, 16, 16, 41, 46, 46, 46, 46, 46, 46, 46, 6, 6, 6, 6, 6, 6, 9, 2, 2, 2, 2, 2, 2, 2, 2, 3, 6, 10, 10, 10, 17, 41, 41, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 6, 9, 9, 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, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 233) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/233 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/233' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322762.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184322762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322762 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 3, 6, 6, 6, 13, 6, 6, 15, 14, 14, 40, 46, 46, 46, 46, 46, 46, 46, 6, 6, 6, 6, 6, 6, 12, 4, 4, 4, 4, 4, 4, 4, 4, 3, 6, 13, 13, 13, 15, 40, 40, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 6, 12, 12, 12, 12, 12] 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]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184322762 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762 Building ZINC001184322762 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184322762 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 230) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/230: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322762.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184322762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322762 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 6, 10, 6, 6, 17, 16, 16, 41, 46, 46, 46, 46, 46, 46, 46, 6, 6, 6, 6, 6, 6, 9, 2, 2, 2, 2, 2, 2, 2, 2, 3, 6, 10, 10, 10, 17, 41, 41, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 6, 9, 9, 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, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 231) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/231: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322762.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184322762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322762 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 3, 6, 6, 6, 13, 6, 6, 15, 14, 14, 40, 46, 46, 46, 46, 46, 46, 46, 6, 6, 6, 6, 6, 6, 12, 4, 4, 4, 4, 4, 4, 4, 4, 3, 6, 13, 13, 13, 15, 40, 40, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 6, 12, 12, 12, 12, 12] 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]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 232) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/232: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322762.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184322762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322762 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 6, 10, 6, 6, 17, 16, 16, 41, 46, 46, 46, 46, 46, 46, 46, 6, 6, 6, 6, 6, 6, 9, 2, 2, 2, 2, 2, 2, 2, 2, 3, 6, 10, 10, 10, 17, 41, 41, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 6, 9, 9, 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, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 233) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/233: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322762.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184322762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322762 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 3, 6, 6, 6, 13, 6, 6, 15, 14, 14, 40, 46, 46, 46, 46, 46, 46, 46, 6, 6, 6, 6, 6, 6, 12, 4, 4, 4, 4, 4, 4, 4, 4, 3, 6, 13, 13, 13, 15, 40, 40, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 6, 12, 12, 12, 12, 12] 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]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184322762 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762 Building ZINC001184322762 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184322762 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 230) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/230: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322762.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184322762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322762 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 6, 10, 6, 6, 17, 16, 16, 41, 46, 46, 46, 46, 46, 46, 46, 6, 6, 6, 6, 6, 6, 9, 2, 2, 2, 2, 2, 2, 2, 2, 3, 6, 10, 10, 10, 17, 41, 41, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 6, 9, 9, 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, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 231) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/231: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322762.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184322762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322762 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 3, 6, 6, 6, 13, 6, 6, 15, 14, 14, 40, 46, 46, 46, 46, 46, 46, 46, 6, 6, 6, 6, 6, 6, 12, 4, 4, 4, 4, 4, 4, 4, 4, 3, 6, 13, 13, 13, 15, 40, 40, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 6, 12, 12, 12, 12, 12] 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]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 232) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/232: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322762.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184322762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322762 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 6, 10, 6, 6, 17, 16, 16, 41, 46, 46, 46, 46, 46, 46, 46, 6, 6, 6, 6, 6, 6, 9, 2, 2, 2, 2, 2, 2, 2, 2, 3, 6, 10, 10, 10, 17, 41, 41, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 6, 9, 9, 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, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 233) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/233: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322762.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184322762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322762 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 3, 6, 6, 6, 13, 6, 6, 15, 14, 14, 40, 46, 46, 46, 46, 46, 46, 46, 6, 6, 6, 6, 6, 6, 12, 4, 4, 4, 4, 4, 4, 4, 4, 3, 6, 13, 13, 13, 15, 40, 40, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 6, 12, 12, 12, 12, 12] 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]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184322762 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762 Building ZINC001184322762 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184322762 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 230) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/230: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322762.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184322762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322762 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 6, 10, 6, 6, 17, 16, 16, 41, 46, 46, 46, 46, 46, 46, 46, 6, 6, 6, 6, 6, 6, 9, 2, 2, 2, 2, 2, 2, 2, 2, 3, 6, 10, 10, 10, 17, 41, 41, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 6, 9, 9, 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, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 231) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/231: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322762.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184322762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322762 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 3, 6, 6, 6, 13, 6, 6, 15, 14, 14, 40, 46, 46, 46, 46, 46, 46, 46, 6, 6, 6, 6, 6, 6, 12, 4, 4, 4, 4, 4, 4, 4, 4, 3, 6, 13, 13, 13, 15, 40, 40, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 6, 12, 12, 12, 12, 12] 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]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 232) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/232: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322762.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184322762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322762 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 6, 10, 6, 6, 17, 16, 16, 41, 46, 46, 46, 46, 46, 46, 46, 6, 6, 6, 6, 6, 6, 9, 2, 2, 2, 2, 2, 2, 2, 2, 3, 6, 10, 10, 10, 17, 41, 41, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 6, 9, 9, 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, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 233) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/233: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322762.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184322762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322762 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 3, 6, 6, 6, 13, 6, 6, 15, 14, 14, 40, 46, 46, 46, 46, 46, 46, 46, 6, 6, 6, 6, 6, 6, 12, 4, 4, 4, 4, 4, 4, 4, 4, 3, 6, 13, 13, 13, 15, 40, 40, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 6, 12, 12, 12, 12, 12] 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]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184322762 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322762 Building ZINC001184322764 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184322764 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 234) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/234 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/234' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322764.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184322764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322764 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 5, 5, 5, 9, 5, 5, 16, 15, 15, 42, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 9, 9, 9, 16, 42, 42, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 9, 9, 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, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 235) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/235 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/235' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322764.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184322764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322764 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 5, 9, 5, 5, 15, 14, 14, 41, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 9, 2, 2, 2, 2, 2, 2, 2, 2, 3, 5, 9, 9, 9, 15, 41, 41, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 9, 9, 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, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 236) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/236 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/236' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322764.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184322764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322764 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 5, 5, 5, 9, 5, 5, 16, 15, 15, 42, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 9, 9, 9, 16, 42, 42, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 9, 9, 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, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 237) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/237 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/237' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322764.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184322764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322764 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 5, 9, 5, 5, 15, 14, 14, 41, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 9, 2, 2, 2, 2, 2, 2, 2, 2, 3, 5, 9, 9, 9, 15, 41, 41, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 9, 9, 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, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184322764 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764 Building ZINC001184322764 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184322764 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 234) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322764.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184322764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322764 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 5, 5, 5, 9, 5, 5, 16, 15, 15, 42, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 9, 9, 9, 16, 42, 42, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 9, 9, 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, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 235) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322764.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184322764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322764 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 5, 9, 5, 5, 15, 14, 14, 41, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 9, 2, 2, 2, 2, 2, 2, 2, 2, 3, 5, 9, 9, 9, 15, 41, 41, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 9, 9, 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, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 236) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/236: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322764.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184322764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322764 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 5, 5, 5, 9, 5, 5, 16, 15, 15, 42, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 9, 9, 9, 16, 42, 42, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 9, 9, 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, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 237) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/237: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322764.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184322764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322764 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 5, 9, 5, 5, 15, 14, 14, 41, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 9, 2, 2, 2, 2, 2, 2, 2, 2, 3, 5, 9, 9, 9, 15, 41, 41, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 9, 9, 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, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184322764 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764 Building ZINC001184322764 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184322764 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 234) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322764.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184322764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322764 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 5, 5, 5, 9, 5, 5, 16, 15, 15, 42, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 9, 9, 9, 16, 42, 42, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 9, 9, 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, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 235) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322764.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184322764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322764 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 5, 9, 5, 5, 15, 14, 14, 41, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 9, 2, 2, 2, 2, 2, 2, 2, 2, 3, 5, 9, 9, 9, 15, 41, 41, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 9, 9, 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, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 236) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/236: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322764.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184322764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322764 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 5, 5, 5, 9, 5, 5, 16, 15, 15, 42, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 9, 9, 9, 16, 42, 42, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 9, 9, 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, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 237) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/237: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322764.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184322764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322764 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 5, 9, 5, 5, 15, 14, 14, 41, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 9, 2, 2, 2, 2, 2, 2, 2, 2, 3, 5, 9, 9, 9, 15, 41, 41, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 9, 9, 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, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184322764 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764 Building ZINC001184322764 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184322764 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 234) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322764.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184322764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322764 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 5, 5, 5, 9, 5, 5, 16, 15, 15, 42, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 9, 9, 9, 16, 42, 42, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 9, 9, 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, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 235) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322764.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184322764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322764 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 5, 9, 5, 5, 15, 14, 14, 41, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 9, 2, 2, 2, 2, 2, 2, 2, 2, 3, 5, 9, 9, 9, 15, 41, 41, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 9, 9, 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, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 236) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/236: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322764.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184322764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322764 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 5, 5, 5, 9, 5, 5, 16, 15, 15, 42, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 9, 9, 9, 16, 42, 42, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 9, 9, 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, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 237) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/237: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322764.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184322764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322764 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 5, 9, 5, 5, 15, 14, 14, 41, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 9, 2, 2, 2, 2, 2, 2, 2, 2, 3, 5, 9, 9, 9, 15, 41, 41, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 9, 9, 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, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184322764 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322764 Building ZINC001184322767 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184322767 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 238) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/238 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/238' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322767.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184322767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322767 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 5, 9, 5, 5, 14, 13, 13, 42, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 9, 2, 2, 2, 2, 2, 2, 2, 2, 3, 5, 9, 9, 9, 14, 42, 42, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 9, 9, 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, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 239) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/239 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/239' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322767.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184322767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322767 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 5, 10, 5, 5, 15, 14, 14, 39, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 9, 2, 2, 2, 2, 2, 2, 2, 2, 3, 5, 10, 10, 10, 15, 39, 39, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 9, 9, 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, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 240) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/240 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/240' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322767.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184322767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322767 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 5, 9, 5, 5, 14, 13, 13, 42, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 9, 2, 2, 2, 2, 2, 2, 2, 2, 3, 5, 9, 9, 9, 14, 42, 42, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 9, 9, 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, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 241) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/241 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/241' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322767.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184322767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322767 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 5, 10, 5, 5, 15, 14, 14, 39, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 9, 2, 2, 2, 2, 2, 2, 2, 2, 3, 5, 10, 10, 10, 15, 39, 39, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 9, 9, 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, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184322767 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767 Building ZINC001184322767 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184322767 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 238) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322767.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184322767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322767 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 5, 9, 5, 5, 14, 13, 13, 42, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 9, 2, 2, 2, 2, 2, 2, 2, 2, 3, 5, 9, 9, 9, 14, 42, 42, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 9, 9, 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, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 239) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322767.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184322767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322767 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 5, 10, 5, 5, 15, 14, 14, 39, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 9, 2, 2, 2, 2, 2, 2, 2, 2, 3, 5, 10, 10, 10, 15, 39, 39, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 9, 9, 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, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 240) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/240: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322767.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184322767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322767 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 5, 9, 5, 5, 14, 13, 13, 42, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 9, 2, 2, 2, 2, 2, 2, 2, 2, 3, 5, 9, 9, 9, 14, 42, 42, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 9, 9, 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, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 241) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/241: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322767.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184322767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322767 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 5, 10, 5, 5, 15, 14, 14, 39, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 9, 2, 2, 2, 2, 2, 2, 2, 2, 3, 5, 10, 10, 10, 15, 39, 39, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 9, 9, 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, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184322767 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767 Building ZINC001184322767 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184322767 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 238) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322767.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184322767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322767 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 5, 9, 5, 5, 14, 13, 13, 42, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 9, 2, 2, 2, 2, 2, 2, 2, 2, 3, 5, 9, 9, 9, 14, 42, 42, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 9, 9, 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, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 239) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322767.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184322767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322767 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 5, 10, 5, 5, 15, 14, 14, 39, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 9, 2, 2, 2, 2, 2, 2, 2, 2, 3, 5, 10, 10, 10, 15, 39, 39, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 9, 9, 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, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 240) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/240: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322767.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184322767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322767 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 5, 9, 5, 5, 14, 13, 13, 42, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 9, 2, 2, 2, 2, 2, 2, 2, 2, 3, 5, 9, 9, 9, 14, 42, 42, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 9, 9, 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, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 241) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/241: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322767.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184322767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322767 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 5, 10, 5, 5, 15, 14, 14, 39, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 9, 2, 2, 2, 2, 2, 2, 2, 2, 3, 5, 10, 10, 10, 15, 39, 39, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 9, 9, 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, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184322767 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767 Building ZINC001184322767 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184322767 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 238) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322767.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184322767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322767 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 5, 9, 5, 5, 14, 13, 13, 42, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 9, 2, 2, 2, 2, 2, 2, 2, 2, 3, 5, 9, 9, 9, 14, 42, 42, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 9, 9, 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, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 239) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322767.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184322767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322767 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 5, 10, 5, 5, 15, 14, 14, 39, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 9, 2, 2, 2, 2, 2, 2, 2, 2, 3, 5, 10, 10, 10, 15, 39, 39, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 9, 9, 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, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 240) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/240: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322767.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184322767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322767 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 5, 9, 5, 5, 14, 13, 13, 42, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 9, 2, 2, 2, 2, 2, 2, 2, 2, 3, 5, 9, 9, 9, 14, 42, 42, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 9, 9, 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, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 241) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/241: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC) `ZINC001184322767.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184322767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184322767 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1cc(OC)c(C(=O)NC[C@H]2CCCN2CC)cc1S(=O)(=O)CC 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', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 1, 1, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 5, 10, 5, 5, 15, 14, 14, 39, 48, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 9, 2, 2, 2, 2, 2, 2, 2, 2, 3, 5, 10, 10, 10, 15, 39, 39, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 9, 9, 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, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184322767 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184322767 Building ZINC001184324860 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184324860' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184324860 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184324860 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184324860/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184324860 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 242) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/242 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/242' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)Nc1nonc1c1noc(=O)n1c1ccc(F)c(Br)c1) `ZINC001184324860.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184324860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184324860/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001184324860 none CC(C)C[C@@]([O-])([SiH3])C(=O)Nc1nonc1c1noc(=O)n1c1ccc(F)c(Br)c1 NO_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', 'O.3', 'N.2', 'C.2', 'C.2', 'N.2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'H', 'H', '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, 12, 8, 1, 1, 8, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 27, 27, 27, 27, 23, 27, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184324860 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184324860/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184324860 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 243) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/243 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/243' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)Nc1nonc1c1noc(=O)n1c1ccc(F)c(Br)c1) `ZINC001184324860.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184324860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184324860/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001184324860 none CC(C)C[C@]([O-])([SiH3])C(=O)Nc1nonc1c1noc(=O)n1c1ccc(F)c(Br)c1 NO_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', 'O.3', 'N.2', 'C.2', 'C.2', 'N.2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'H', 'H', '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, 12, 8, 1, 1, 8, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 25, 25, 25, 25, 23, 25, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 37, 35, 7, 36, 28, 29, 30, 31] set([38, 39, 40, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184324860 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184324860 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184324860/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184324860/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184324860 Building ZINC001184324860 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184324860' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184324860 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184324860 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184324860/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184324860 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 242) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC(C)C[C@@]([O-])([SiH3])C(=O)Nc1nonc1c1noc(=O)n1c1ccc(F)c(Br)c1) `ZINC001184324860.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184324860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184324860/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001184324860 none CC(C)C[C@@]([O-])([SiH3])C(=O)Nc1nonc1c1noc(=O)n1c1ccc(F)c(Br)c1 NO_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', 'O.3', 'N.2', 'C.2', 'C.2', 'N.2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'H', 'H', '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, 12, 8, 1, 1, 8, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 27, 27, 27, 27, 23, 27, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184324860 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184324860/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184324860 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 243) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC(C)C[C@]([O-])([SiH3])C(=O)Nc1nonc1c1noc(=O)n1c1ccc(F)c(Br)c1) `ZINC001184324860.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184324860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184324860/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001184324860 none CC(C)C[C@]([O-])([SiH3])C(=O)Nc1nonc1c1noc(=O)n1c1ccc(F)c(Br)c1 NO_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', 'O.3', 'N.2', 'C.2', 'C.2', 'N.2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'H', 'H', '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, 12, 8, 1, 1, 8, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 25, 25, 25, 25, 23, 25, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 37, 35, 7, 36, 28, 29, 30, 31] set([38, 39, 40, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184324860 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184324860 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184324860/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184324860/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184324860 Building ZINC001184324906 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184324906' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184324906 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184324906 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184324906/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184324906 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 244) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/244 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/244' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)Nc1ncnc2c1ncn2CCOC[P@](=O)(O)OCOC(=O)C(C)(C)C) `ZINC001184324906.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184324906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184324906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001184324906 none CC(C)C[C@@]([O-])([SiH3])C(=O)Nc1ncnc2c1ncn2CCOC[P@](=O)(O)OCOC(=O)C(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', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'P.3', 'O.2', 'O.3', 'O.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 5, 5, 12, 5, 13, 11, 12, 12, 5, 12, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 5, 4, 3, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 12, 17, 25, 35, 35, 35, 41, 49, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 10, 12, 12, 25, 25, 35, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 39, 40, 41, 42, 7, 2, 8, 3, 43, 9, 4, 6, 5] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184324906 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184324906/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184324906 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 245) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/245 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/245' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)Nc1ncnc2c1ncn2CCOC[P@](=O)(O)OCOC(=O)C(C)(C)C) `ZINC001184324906.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184324906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184324906/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001184324906 none CC(C)C[C@]([O-])([SiH3])C(=O)Nc1ncnc2c1ncn2CCOC[P@](=O)(O)OCOC(=O)C(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', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'P.3', 'O.2', 'O.3', 'O.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 5, 5, 12, 5, 13, 11, 12, 12, 5, 12, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 5, 4, 3, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 13, 22, 26, 35, 35, 35, 39, 48, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 11, 13, 13, 26, 26, 35, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 39, 40, 41, 42, 7, 2, 8, 3, 43, 9, 4, 6, 5] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184324906 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184324906 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184324906/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184324906/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184324906 Building ZINC001184324906 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184324906' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184324906 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184324906 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184324906/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184324906 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 244) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC(C)C[C@@]([O-])([SiH3])C(=O)Nc1ncnc2c1ncn2CCOC[P@](=O)(O)OCOC(=O)C(C)(C)C) `ZINC001184324906.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184324906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184324906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001184324906 none CC(C)C[C@@]([O-])([SiH3])C(=O)Nc1ncnc2c1ncn2CCOC[P@](=O)(O)OCOC(=O)C(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', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'P.3', 'O.2', 'O.3', 'O.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 5, 5, 12, 5, 13, 11, 12, 12, 5, 12, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 5, 4, 3, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 12, 17, 25, 35, 35, 35, 41, 49, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 10, 12, 12, 25, 25, 35, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 39, 40, 41, 42, 7, 2, 8, 3, 43, 9, 4, 6, 5] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184324906 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184324906/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184324906 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 245) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC(C)C[C@]([O-])([SiH3])C(=O)Nc1ncnc2c1ncn2CCOC[P@](=O)(O)OCOC(=O)C(C)(C)C) `ZINC001184324906.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184324906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184324906/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001184324906 none CC(C)C[C@]([O-])([SiH3])C(=O)Nc1ncnc2c1ncn2CCOC[P@](=O)(O)OCOC(=O)C(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', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'P.3', 'O.2', 'O.3', 'O.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 8, 5, 5, 12, 5, 13, 11, 12, 12, 5, 12, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 5, 4, 3, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 13, 22, 26, 35, 35, 35, 39, 48, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 11, 13, 13, 26, 26, 35, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 39, 40, 41, 42, 7, 2, 8, 3, 43, 9, 4, 6, 5] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184324906 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184324906 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184324906/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184324906/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184324906 Building ZINC001184327693 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327693' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327693 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184327693 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327693/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327693 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 246) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/246 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/246' -> `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[C@H](C(=O)NCCOCCOCCOCc1ccccc1)C(C)C) `ZINC001184327693.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184327693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 73 natoms 72 natoms 71 natoms 70 names: ZINC001184327693 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N[C@H](C(=O)NCCOCCOCCOCc1ccccc1)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.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 6, 4, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 11, 16, 16, 21, 27, 27, 29, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 16, 16, 16, 16, 27, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 63, 64, 65, 66, 67, 68, 69] set([16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327693 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327693/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327693 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 247) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/247 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/247' -> `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[C@H](C(=O)NCCOCCOCCOCc1ccccc1)C(C)C) `ZINC001184327693.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184327693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327693/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 73 natoms 72 natoms 71 natoms 70 names: ZINC001184327693 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N[C@H](C(=O)NCCOCCOCCOCc1ccccc1)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.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 6, 4, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 14, 14, 21, 26, 26, 29, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 14, 14, 14, 14, 26, 26, 26, 26, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 63, 64, 65, 66, 67, 68, 69] set([16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327693 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184327693 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327693/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327693/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327693 Building ZINC001184327693 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327693' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327693 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184327693 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327693/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327693 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 246) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N[C@H](C(=O)NCCOCCOCCOCc1ccccc1)C(C)C) `ZINC001184327693.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184327693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 73 natoms 72 natoms 71 natoms 70 names: ZINC001184327693 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N[C@H](C(=O)NCCOCCOCCOCc1ccccc1)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.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 6, 4, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 11, 16, 16, 21, 27, 27, 29, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 16, 16, 16, 16, 27, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 63, 64, 65, 66, 67, 68, 69] set([16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327693 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327693/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327693 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 247) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N[C@H](C(=O)NCCOCCOCCOCc1ccccc1)C(C)C) `ZINC001184327693.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184327693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327693/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 73 natoms 72 natoms 71 natoms 70 names: ZINC001184327693 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N[C@H](C(=O)NCCOCCOCCOCc1ccccc1)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.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 6, 4, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 14, 14, 21, 26, 26, 29, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 14, 14, 14, 14, 26, 26, 26, 26, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 63, 64, 65, 66, 67, 68, 69] set([16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327693 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184327693 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327693/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327693/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327693 Building ZINC001184327694 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327694' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327694 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184327694 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327694/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327694 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 248) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/248 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/248' -> `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[C@H](C(=O)NCCOCCOCCOCc1ccccc1)C(C)C) `ZINC001184327694.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184327694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 73 natoms 72 natoms 71 natoms 70 names: ZINC001184327694 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N[C@H](C(=O)NCCOCCOCCOCc1ccccc1)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.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 6, 4, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 10, 15, 15, 20, 26, 26, 29, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 15, 15, 15, 15, 26, 26, 26, 26, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 63, 64, 65, 66, 67, 68, 69] set([16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327694 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327694/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327694 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 249) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/249 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/249' -> `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[C@H](C(=O)NCCOCCOCCOCc1ccccc1)C(C)C) `ZINC001184327694.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184327694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327694/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 73 natoms 72 natoms 71 natoms 70 names: ZINC001184327694 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)N[C@H](C(=O)NCCOCCOCCOCc1ccccc1)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.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 6, 4, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 9, 14, 14, 21, 24, 24, 26, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 14, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 63, 64, 65, 66, 67, 68, 69] set([16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327694 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184327694 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327694/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327694/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327694 Building ZINC001184327694 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327694' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327694 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184327694 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327694/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327694 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 248) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N[C@H](C(=O)NCCOCCOCCOCc1ccccc1)C(C)C) `ZINC001184327694.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184327694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 73 natoms 72 natoms 71 natoms 70 names: ZINC001184327694 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N[C@H](C(=O)NCCOCCOCCOCc1ccccc1)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.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 6, 4, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 10, 15, 15, 20, 26, 26, 29, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 15, 15, 15, 15, 26, 26, 26, 26, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 63, 64, 65, 66, 67, 68, 69] set([16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327694 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327694/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327694 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 249) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC[C@H](C)[C@]([O-])([SiH3])C(=O)N[C@H](C(=O)NCCOCCOCCOCc1ccccc1)C(C)C) `ZINC001184327694.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184327694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327694/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 73 natoms 72 natoms 71 natoms 70 names: ZINC001184327694 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)N[C@H](C(=O)NCCOCCOCCOCc1ccccc1)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.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 6, 4, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 9, 14, 14, 21, 24, 24, 26, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 14, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 63, 64, 65, 66, 67, 68, 69] set([16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327694 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184327694 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327694/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327694/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327694 Building ZINC001184327859 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327859' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327859 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184327859 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327859/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327859 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 250) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/250 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/250' -> `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[C@@H](Cc1ccccc1)C(=O)N[C@@H](Cc1c[nH]c2ccccc12)C(N)=O) `ZINC001184327859.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184327859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184327859 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@@H](Cc1c[nH]c2ccccc12)C(N)=O 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', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 7, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 8, 8, 12, 12, 12, 12, 12, 12, 8, 13, 13, 13, 21, 21, 38, 47, 47, 47, 47, 47, 47, 47, 47, 47, 21, 35, 36, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 13, 38, 38, 47, 47, 47, 47, 47, 36, 36] 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]) total number of confs: 287 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327859 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327859/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327859 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 251) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/251 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/251' -> `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[C@@H](Cc1ccccc1)C(=O)N[C@@H](Cc1c[nH]c2ccccc12)C(N)=O) `ZINC001184327859.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184327859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327859/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184327859 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@@H](Cc1c[nH]c2ccccc12)C(N)=O 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', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 7, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 9, 9, 9, 9, 9, 9, 6, 12, 12, 12, 23, 23, 36, 47, 47, 47, 47, 47, 47, 47, 47, 47, 23, 37, 38, 2, 2, 2, 2, 2, 2, 2, 2, 3, 9, 9, 9, 9, 9, 9, 9, 12, 36, 36, 47, 47, 47, 47, 47, 38, 37] 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]) total number of confs: 271 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327859 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184327859 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327859/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327859/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327859 Building ZINC001184327859 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327859' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327859 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184327859 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327859/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327859 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 250) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@@H](Cc1c[nH]c2ccccc12)C(N)=O) `ZINC001184327859.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184327859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184327859 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@@H](Cc1c[nH]c2ccccc12)C(N)=O 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', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 7, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 8, 8, 12, 12, 12, 12, 12, 12, 8, 13, 13, 13, 21, 21, 38, 47, 47, 47, 47, 47, 47, 47, 47, 47, 21, 35, 36, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 13, 38, 38, 47, 47, 47, 47, 47, 36, 36] 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]) total number of confs: 287 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327859 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327859/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327859 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 251) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC[C@H](C)[C@]([O-])([SiH3])C(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@@H](Cc1c[nH]c2ccccc12)C(N)=O) `ZINC001184327859.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184327859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327859/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184327859 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@@H](Cc1c[nH]c2ccccc12)C(N)=O 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', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 7, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 9, 9, 9, 9, 9, 9, 6, 12, 12, 12, 23, 23, 36, 47, 47, 47, 47, 47, 47, 47, 47, 47, 23, 37, 38, 2, 2, 2, 2, 2, 2, 2, 2, 3, 9, 9, 9, 9, 9, 9, 9, 12, 36, 36, 47, 47, 47, 47, 47, 38, 37] 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]) total number of confs: 271 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327859 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184327859 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327859/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327859/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327859 Building ZINC001184327862 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327862' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327862 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184327862 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327862/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327862 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 252) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/252 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/252' -> `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[C@@H](Cc1ccccc1)C(=O)N[C@@H](Cc1c[nH]c2ccccc12)C(N)=O) `ZINC001184327862.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184327862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327862/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184327862 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@@H](Cc1c[nH]c2ccccc12)C(N)=O 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', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 7, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 3, 8, 8, 13, 13, 13, 13, 13, 13, 8, 13, 13, 13, 21, 21, 38, 48, 48, 48, 48, 48, 48, 48, 48, 48, 21, 36, 37, 4, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 13, 13, 13, 13, 13, 13, 38, 38, 48, 48, 48, 48, 48, 37, 36] 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]) total number of confs: 300 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327862 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327862/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327862 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 253) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/253 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/253' -> `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[C@@H](Cc1ccccc1)C(=O)N[C@@H](Cc1c[nH]c2ccccc12)C(N)=O) `ZINC001184327862.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184327862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327862/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184327862 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@@H](Cc1c[nH]c2ccccc12)C(N)=O 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', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 7, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 11, 11, 11, 11, 11, 11, 7, 12, 12, 12, 24, 24, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 34, 35, 2, 2, 2, 2, 2, 2, 2, 2, 3, 11, 11, 11, 11, 11, 11, 11, 12, 39, 39, 50, 50, 50, 50, 50, 35, 34] 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]) total number of confs: 279 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327862 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184327862 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327862/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327862/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327862 Building ZINC001184327862 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327862' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327862 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184327862 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327862/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327862 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 252) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@@H](Cc1c[nH]c2ccccc12)C(N)=O) `ZINC001184327862.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184327862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327862/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184327862 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@@H](Cc1c[nH]c2ccccc12)C(N)=O 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', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 7, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 3, 8, 8, 13, 13, 13, 13, 13, 13, 8, 13, 13, 13, 21, 21, 38, 48, 48, 48, 48, 48, 48, 48, 48, 48, 21, 36, 37, 4, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 13, 13, 13, 13, 13, 13, 38, 38, 48, 48, 48, 48, 48, 37, 36] 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]) total number of confs: 300 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327862 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327862/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327862 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 253) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@@H](Cc1c[nH]c2ccccc12)C(N)=O) `ZINC001184327862.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184327862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327862/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184327862 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@@H](Cc1c[nH]c2ccccc12)C(N)=O 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', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 7, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 11, 11, 11, 11, 11, 11, 7, 12, 12, 12, 24, 24, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 34, 35, 2, 2, 2, 2, 2, 2, 2, 2, 3, 11, 11, 11, 11, 11, 11, 11, 12, 39, 39, 50, 50, 50, 50, 50, 35, 34] 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]) total number of confs: 279 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327862 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184327862 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327862/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327862/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184327862 Building ZINC001184330143 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184330143' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184330143 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184330143 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184330143/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184330143 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 254) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/254 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/254' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)O[C@H]2c3nccnc3C(=O)N2c2ccc(Cl)cn2)CC1) `ZINC001184330143.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184330143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184330143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184330143 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)O[C@H]2c3nccnc3C(=O)N2c2ccc(Cl)cn2)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', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 7, 1, 8, 1, 1, 8, 1, 1, 11, 8, 1, 1, 1, 1, 16, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 2, 4, 8, 14, 14, 14, 14, 27, 27, 39, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 50, 50, 50, 50, 50, 50, 14, 14, 2, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14, 45, 45, 50, 50, 50, 14, 14, 14, 14] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184330143 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184330143/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184330143 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 255) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/255 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/255' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)O[C@H]2c3nccnc3C(=O)N2c2ccc(Cl)cn2)CC1) `ZINC001184330143.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184330143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184330143/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184330143 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)O[C@H]2c3nccnc3C(=O)N2c2ccc(Cl)cn2)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', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 7, 1, 8, 1, 1, 8, 1, 1, 11, 8, 1, 1, 1, 1, 16, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 2, 6, 12, 17, 17, 17, 17, 25, 25, 41, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 50, 50, 50, 50, 50, 50, 17, 17, 2, 2, 2, 2, 2, 2, 2, 2, 2, 17, 17, 17, 17, 46, 46, 50, 50, 50, 17, 17, 17, 17] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 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: 118 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184330143 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184330143 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184330143/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184330143/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184330143 Building ZINC001184330143 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184330143' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184330143 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184330143 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184330143/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184330143 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 254) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)O[C@H]2c3nccnc3C(=O)N2c2ccc(Cl)cn2)CC1) `ZINC001184330143.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184330143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184330143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184330143 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)O[C@H]2c3nccnc3C(=O)N2c2ccc(Cl)cn2)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', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 7, 1, 8, 1, 1, 8, 1, 1, 11, 8, 1, 1, 1, 1, 16, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 2, 4, 8, 14, 14, 14, 14, 27, 27, 39, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 50, 50, 50, 50, 50, 50, 14, 14, 2, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14, 45, 45, 50, 50, 50, 14, 14, 14, 14] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184330143 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184330143/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184330143 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 255) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC(C)C[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)O[C@H]2c3nccnc3C(=O)N2c2ccc(Cl)cn2)CC1) `ZINC001184330143.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184330143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184330143/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184330143 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)O[C@H]2c3nccnc3C(=O)N2c2ccc(Cl)cn2)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', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 7, 1, 8, 1, 1, 8, 1, 1, 11, 8, 1, 1, 1, 1, 16, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 2, 6, 12, 17, 17, 17, 17, 25, 25, 41, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 50, 50, 50, 50, 50, 50, 17, 17, 2, 2, 2, 2, 2, 2, 2, 2, 2, 17, 17, 17, 17, 46, 46, 50, 50, 50, 17, 17, 17, 17] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 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: 118 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184330143 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184330143 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184330143/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184330143/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184330143 Building ZINC001184330144 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184330144' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184330144 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184330144 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184330144/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184330144 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 256) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/256 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/256' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)O[C@@H]2c3nccnc3C(=O)N2c2ccc(Cl)cn2)CC1) `ZINC001184330144.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184330144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184330144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184330144 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)O[C@@H]2c3nccnc3C(=O)N2c2ccc(Cl)cn2)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', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 7, 1, 8, 1, 1, 8, 1, 1, 11, 8, 1, 1, 1, 1, 16, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 2, 5, 9, 15, 15, 15, 15, 26, 26, 40, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 49, 49, 49, 49, 49, 49, 15, 15, 2, 2, 2, 2, 2, 2, 2, 2, 2, 15, 15, 15, 15, 46, 46, 49, 49, 49, 15, 15, 15, 15] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184330144 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184330144/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184330144 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 257) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/257 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/257' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)O[C@@H]2c3nccnc3C(=O)N2c2ccc(Cl)cn2)CC1) `ZINC001184330144.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184330144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184330144/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184330144 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)O[C@@H]2c3nccnc3C(=O)N2c2ccc(Cl)cn2)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', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 7, 1, 8, 1, 1, 8, 1, 1, 11, 8, 1, 1, 1, 1, 16, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 2, 4, 8, 15, 15, 15, 15, 25, 25, 40, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 50, 50, 50, 50, 50, 50, 15, 15, 2, 2, 2, 2, 2, 2, 2, 2, 2, 15, 15, 15, 15, 47, 47, 50, 50, 50, 15, 15, 15, 15] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 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: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184330144 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184330144 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184330144/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184330144/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184330144 Building ZINC001184330144 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184330144' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184330144 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184330144 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184330144/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184330144 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 256) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)O[C@@H]2c3nccnc3C(=O)N2c2ccc(Cl)cn2)CC1) `ZINC001184330144.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184330144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184330144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184330144 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)O[C@@H]2c3nccnc3C(=O)N2c2ccc(Cl)cn2)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', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 7, 1, 8, 1, 1, 8, 1, 1, 11, 8, 1, 1, 1, 1, 16, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 2, 5, 9, 15, 15, 15, 15, 26, 26, 40, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 49, 49, 49, 49, 49, 49, 15, 15, 2, 2, 2, 2, 2, 2, 2, 2, 2, 15, 15, 15, 15, 46, 46, 49, 49, 49, 15, 15, 15, 15] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184330144 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184330144/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184330144 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 257) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC(C)C[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)O[C@@H]2c3nccnc3C(=O)N2c2ccc(Cl)cn2)CC1) `ZINC001184330144.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184330144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184330144/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184330144 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)O[C@@H]2c3nccnc3C(=O)N2c2ccc(Cl)cn2)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', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 7, 1, 8, 1, 1, 8, 1, 1, 11, 8, 1, 1, 1, 1, 16, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 2, 4, 8, 15, 15, 15, 15, 25, 25, 40, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 50, 50, 50, 50, 50, 50, 15, 15, 2, 2, 2, 2, 2, 2, 2, 2, 2, 15, 15, 15, 15, 47, 47, 50, 50, 50, 15, 15, 15, 15] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 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: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184330144 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184330144 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184330144/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184330144/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184330144 Building ZINC001184331524 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184331524 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 258) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/258 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/258' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])CC(C)C)cc1OC) `ZINC001184331524.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184331524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001184331524 none CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])CC(C)C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 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: [44, 44, 44, 44, 44, 44, 35, 44, 9, 9, 3, 9, 3, 3, 3, 3, 4, 4, 4, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 35, 35, 9, 3, 9, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6] 50 rigid atoms, others: [59, 60, 61, 56, 58, 57, 22, 55, 24, 25, 26, 27, 28, 29, 62, 63] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 64, 65, 66, 67]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 259) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/259 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/259' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])CC(C)C)cc1OC) `ZINC001184331524.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184331524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001184331524 none CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])CC(C)C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 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: [44, 44, 44, 44, 44, 44, 35, 44, 9, 9, 3, 9, 3, 3, 3, 3, 4, 4, 4, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 35, 35, 9, 3, 9, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6] 50 rigid atoms, others: [59, 60, 61, 56, 58, 57, 22, 55, 24, 25, 26, 27, 28, 29, 62, 63] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 64, 65, 66, 67]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 260) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/260 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/260' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])CC(C)C)cc1OC) `ZINC001184331524.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184331524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001184331524 none CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])CC(C)C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 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: [45, 45, 45, 45, 45, 45, 31, 45, 10, 10, 3, 10, 3, 3, 3, 3, 5, 5, 5, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 31, 31, 10, 3, 11, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5] 50 rigid atoms, others: [59, 60, 61, 56, 58, 57, 22, 55, 24, 25, 26, 27, 28, 29, 62, 63] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 64, 65, 66, 67]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 261) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/261 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/261' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])CC(C)C)cc1OC) `ZINC001184331524.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184331524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001184331524 none CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])CC(C)C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 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: [45, 45, 45, 45, 45, 45, 31, 45, 10, 10, 3, 10, 3, 3, 3, 3, 5, 5, 5, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 31, 31, 10, 3, 11, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5] 50 rigid atoms, others: [59, 60, 61, 56, 58, 57, 22, 55, 24, 25, 26, 27, 28, 29, 62, 63] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 64, 65, 66, 67]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184331524 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524 Building ZINC001184331524 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184331524 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 258) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])CC(C)C)cc1OC) `ZINC001184331524.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184331524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001184331524 none CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])CC(C)C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 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: [44, 44, 44, 44, 44, 44, 35, 44, 9, 9, 3, 9, 3, 3, 3, 3, 4, 4, 4, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 35, 35, 9, 3, 9, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6] 50 rigid atoms, others: [59, 60, 61, 56, 58, 57, 22, 55, 24, 25, 26, 27, 28, 29, 62, 63] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 64, 65, 66, 67]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 259) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])CC(C)C)cc1OC) `ZINC001184331524.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184331524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001184331524 none CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])CC(C)C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 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: [44, 44, 44, 44, 44, 44, 35, 44, 9, 9, 3, 9, 3, 3, 3, 3, 4, 4, 4, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 35, 35, 9, 3, 9, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6] 50 rigid atoms, others: [59, 60, 61, 56, 58, 57, 22, 55, 24, 25, 26, 27, 28, 29, 62, 63] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 64, 65, 66, 67]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 260) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/260: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])CC(C)C)cc1OC) `ZINC001184331524.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184331524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001184331524 none CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])CC(C)C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 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: [45, 45, 45, 45, 45, 45, 31, 45, 10, 10, 3, 10, 3, 3, 3, 3, 5, 5, 5, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 31, 31, 10, 3, 11, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5] 50 rigid atoms, others: [59, 60, 61, 56, 58, 57, 22, 55, 24, 25, 26, 27, 28, 29, 62, 63] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 64, 65, 66, 67]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 261) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/261: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])CC(C)C)cc1OC) `ZINC001184331524.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184331524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001184331524 none CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])CC(C)C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 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: [45, 45, 45, 45, 45, 45, 31, 45, 10, 10, 3, 10, 3, 3, 3, 3, 5, 5, 5, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 31, 31, 10, 3, 11, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5] 50 rigid atoms, others: [59, 60, 61, 56, 58, 57, 22, 55, 24, 25, 26, 27, 28, 29, 62, 63] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 64, 65, 66, 67]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184331524 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524 Building ZINC001184331524 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184331524 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 258) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])CC(C)C)cc1OC) `ZINC001184331524.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184331524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001184331524 none CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])CC(C)C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 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: [44, 44, 44, 44, 44, 44, 35, 44, 9, 9, 3, 9, 3, 3, 3, 3, 4, 4, 4, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 35, 35, 9, 3, 9, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6] 50 rigid atoms, others: [59, 60, 61, 56, 58, 57, 22, 55, 24, 25, 26, 27, 28, 29, 62, 63] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 64, 65, 66, 67]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 259) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])CC(C)C)cc1OC) `ZINC001184331524.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184331524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001184331524 none CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])CC(C)C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 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: [44, 44, 44, 44, 44, 44, 35, 44, 9, 9, 3, 9, 3, 3, 3, 3, 4, 4, 4, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 35, 35, 9, 3, 9, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6] 50 rigid atoms, others: [59, 60, 61, 56, 58, 57, 22, 55, 24, 25, 26, 27, 28, 29, 62, 63] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 64, 65, 66, 67]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 260) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/260: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])CC(C)C)cc1OC) `ZINC001184331524.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184331524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001184331524 none CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])CC(C)C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 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: [45, 45, 45, 45, 45, 45, 31, 45, 10, 10, 3, 10, 3, 3, 3, 3, 5, 5, 5, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 31, 31, 10, 3, 11, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5] 50 rigid atoms, others: [59, 60, 61, 56, 58, 57, 22, 55, 24, 25, 26, 27, 28, 29, 62, 63] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 64, 65, 66, 67]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 261) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/261: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])CC(C)C)cc1OC) `ZINC001184331524.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184331524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001184331524 none CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])CC(C)C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 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: [45, 45, 45, 45, 45, 45, 31, 45, 10, 10, 3, 10, 3, 3, 3, 3, 5, 5, 5, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 31, 31, 10, 3, 11, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5] 50 rigid atoms, others: [59, 60, 61, 56, 58, 57, 22, 55, 24, 25, 26, 27, 28, 29, 62, 63] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 64, 65, 66, 67]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184331524 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524 Building ZINC001184331524 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184331524 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 258) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])CC(C)C)cc1OC) `ZINC001184331524.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184331524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001184331524 none CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])CC(C)C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 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: [44, 44, 44, 44, 44, 44, 35, 44, 9, 9, 3, 9, 3, 3, 3, 3, 4, 4, 4, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 35, 35, 9, 3, 9, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6] 50 rigid atoms, others: [59, 60, 61, 56, 58, 57, 22, 55, 24, 25, 26, 27, 28, 29, 62, 63] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 64, 65, 66, 67]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 259) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])CC(C)C)cc1OC) `ZINC001184331524.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184331524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001184331524 none CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])CC(C)C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 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: [44, 44, 44, 44, 44, 44, 35, 44, 9, 9, 3, 9, 3, 3, 3, 3, 4, 4, 4, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 35, 35, 9, 3, 9, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6] 50 rigid atoms, others: [59, 60, 61, 56, 58, 57, 22, 55, 24, 25, 26, 27, 28, 29, 62, 63] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 64, 65, 66, 67]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 260) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/260: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])CC(C)C)cc1OC) `ZINC001184331524.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184331524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001184331524 none CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])CC(C)C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 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: [45, 45, 45, 45, 45, 45, 31, 45, 10, 10, 3, 10, 3, 3, 3, 3, 5, 5, 5, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 31, 31, 10, 3, 11, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5] 50 rigid atoms, others: [59, 60, 61, 56, 58, 57, 22, 55, 24, 25, 26, 27, 28, 29, 62, 63] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 64, 65, 66, 67]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 261) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/261: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])CC(C)C)cc1OC) `ZINC001184331524.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184331524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001184331524 none CCN1CCC[C@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])CC(C)C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 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: [45, 45, 45, 45, 45, 45, 31, 45, 10, 10, 3, 10, 3, 3, 3, 3, 5, 5, 5, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 31, 31, 10, 3, 11, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5] 50 rigid atoms, others: [59, 60, 61, 56, 58, 57, 22, 55, 24, 25, 26, 27, 28, 29, 62, 63] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 64, 65, 66, 67]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184331524 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331524 Building ZINC001184331525 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184331525 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 262) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/262 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/262' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])CC(C)C)cc1OC) `ZINC001184331525.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184331525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001184331525 none CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])CC(C)C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 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: [44, 44, 44, 44, 44, 44, 31, 44, 9, 9, 3, 9, 3, 3, 3, 3, 5, 5, 5, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 31, 31, 9, 3, 9, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5] 50 rigid atoms, others: [59, 60, 61, 56, 58, 57, 22, 55, 24, 25, 26, 27, 28, 29, 62, 63] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 64, 65, 66, 67]) total number of confs: 185 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 263) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/263 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/263' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])CC(C)C)cc1OC) `ZINC001184331525.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184331525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001184331525 none CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])CC(C)C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 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: [44, 44, 44, 44, 44, 44, 31, 44, 9, 9, 3, 9, 3, 3, 3, 3, 5, 5, 5, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 31, 31, 9, 3, 9, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5] 50 rigid atoms, others: [59, 60, 61, 56, 58, 57, 22, 55, 24, 25, 26, 27, 28, 29, 62, 63] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 64, 65, 66, 67]) total number of confs: 185 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 264) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/264 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/264' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])CC(C)C)cc1OC) `ZINC001184331525.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184331525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001184331525 none CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])CC(C)C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 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: [46, 46, 46, 46, 46, 46, 29, 46, 7, 7, 3, 7, 3, 3, 3, 3, 4, 4, 4, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 29, 29, 7, 3, 8, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7] 50 rigid atoms, others: [59, 60, 61, 56, 58, 57, 22, 55, 24, 25, 26, 27, 28, 29, 62, 63] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 64, 65, 66, 67]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 265) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/265 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/265' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])CC(C)C)cc1OC) `ZINC001184331525.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184331525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001184331525 none CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])CC(C)C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 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: [46, 46, 46, 46, 46, 46, 29, 46, 7, 7, 3, 7, 3, 3, 3, 3, 4, 4, 4, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 29, 29, 7, 3, 8, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7] 50 rigid atoms, others: [59, 60, 61, 56, 58, 57, 22, 55, 24, 25, 26, 27, 28, 29, 62, 63] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 64, 65, 66, 67]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184331525 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525 Building ZINC001184331525 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184331525 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 262) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])CC(C)C)cc1OC) `ZINC001184331525.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184331525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001184331525 none CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])CC(C)C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 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: [44, 44, 44, 44, 44, 44, 31, 44, 9, 9, 3, 9, 3, 3, 3, 3, 5, 5, 5, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 31, 31, 9, 3, 9, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5] 50 rigid atoms, others: [59, 60, 61, 56, 58, 57, 22, 55, 24, 25, 26, 27, 28, 29, 62, 63] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 64, 65, 66, 67]) total number of confs: 185 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 263) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])CC(C)C)cc1OC) `ZINC001184331525.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184331525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001184331525 none CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])CC(C)C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 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: [44, 44, 44, 44, 44, 44, 31, 44, 9, 9, 3, 9, 3, 3, 3, 3, 5, 5, 5, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 31, 31, 9, 3, 9, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5] 50 rigid atoms, others: [59, 60, 61, 56, 58, 57, 22, 55, 24, 25, 26, 27, 28, 29, 62, 63] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 64, 65, 66, 67]) total number of confs: 185 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 264) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/264: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])CC(C)C)cc1OC) `ZINC001184331525.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184331525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001184331525 none CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])CC(C)C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 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: [46, 46, 46, 46, 46, 46, 29, 46, 7, 7, 3, 7, 3, 3, 3, 3, 4, 4, 4, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 29, 29, 7, 3, 8, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7] 50 rigid atoms, others: [59, 60, 61, 56, 58, 57, 22, 55, 24, 25, 26, 27, 28, 29, 62, 63] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 64, 65, 66, 67]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 265) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/265: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])CC(C)C)cc1OC) `ZINC001184331525.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184331525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001184331525 none CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])CC(C)C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 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: [46, 46, 46, 46, 46, 46, 29, 46, 7, 7, 3, 7, 3, 3, 3, 3, 4, 4, 4, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 29, 29, 7, 3, 8, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7] 50 rigid atoms, others: [59, 60, 61, 56, 58, 57, 22, 55, 24, 25, 26, 27, 28, 29, 62, 63] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 64, 65, 66, 67]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184331525 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525 Building ZINC001184331525 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184331525 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 262) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])CC(C)C)cc1OC) `ZINC001184331525.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184331525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001184331525 none CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])CC(C)C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 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: [44, 44, 44, 44, 44, 44, 31, 44, 9, 9, 3, 9, 3, 3, 3, 3, 5, 5, 5, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 31, 31, 9, 3, 9, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5] 50 rigid atoms, others: [59, 60, 61, 56, 58, 57, 22, 55, 24, 25, 26, 27, 28, 29, 62, 63] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 64, 65, 66, 67]) total number of confs: 185 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 263) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])CC(C)C)cc1OC) `ZINC001184331525.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184331525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001184331525 none CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])CC(C)C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 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: [44, 44, 44, 44, 44, 44, 31, 44, 9, 9, 3, 9, 3, 3, 3, 3, 5, 5, 5, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 31, 31, 9, 3, 9, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5] 50 rigid atoms, others: [59, 60, 61, 56, 58, 57, 22, 55, 24, 25, 26, 27, 28, 29, 62, 63] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 64, 65, 66, 67]) total number of confs: 185 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 264) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/264: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])CC(C)C)cc1OC) `ZINC001184331525.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184331525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001184331525 none CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])CC(C)C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 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: [46, 46, 46, 46, 46, 46, 29, 46, 7, 7, 3, 7, 3, 3, 3, 3, 4, 4, 4, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 29, 29, 7, 3, 8, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7] 50 rigid atoms, others: [59, 60, 61, 56, 58, 57, 22, 55, 24, 25, 26, 27, 28, 29, 62, 63] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 64, 65, 66, 67]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 265) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/265: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])CC(C)C)cc1OC) `ZINC001184331525.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184331525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001184331525 none CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])CC(C)C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 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: [46, 46, 46, 46, 46, 46, 29, 46, 7, 7, 3, 7, 3, 3, 3, 3, 4, 4, 4, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 29, 29, 7, 3, 8, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7] 50 rigid atoms, others: [59, 60, 61, 56, 58, 57, 22, 55, 24, 25, 26, 27, 28, 29, 62, 63] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 64, 65, 66, 67]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184331525 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525 Building ZINC001184331525 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184331525 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 262) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])CC(C)C)cc1OC) `ZINC001184331525.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184331525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001184331525 none CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])CC(C)C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 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: [44, 44, 44, 44, 44, 44, 31, 44, 9, 9, 3, 9, 3, 3, 3, 3, 5, 5, 5, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 31, 31, 9, 3, 9, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5] 50 rigid atoms, others: [59, 60, 61, 56, 58, 57, 22, 55, 24, 25, 26, 27, 28, 29, 62, 63] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 64, 65, 66, 67]) total number of confs: 185 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 263) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])CC(C)C)cc1OC) `ZINC001184331525.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184331525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001184331525 none CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@@]([O-])([SiH3])CC(C)C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 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: [44, 44, 44, 44, 44, 44, 31, 44, 9, 9, 3, 9, 3, 3, 3, 3, 5, 5, 5, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 31, 31, 9, 3, 9, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5] 50 rigid atoms, others: [59, 60, 61, 56, 58, 57, 22, 55, 24, 25, 26, 27, 28, 29, 62, 63] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 64, 65, 66, 67]) total number of confs: 185 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 264) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/264: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])CC(C)C)cc1OC) `ZINC001184331525.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184331525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001184331525 none CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])CC(C)C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 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: [46, 46, 46, 46, 46, 46, 29, 46, 7, 7, 3, 7, 3, 3, 3, 3, 4, 4, 4, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 29, 29, 7, 3, 8, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7] 50 rigid atoms, others: [59, 60, 61, 56, 58, 57, 22, 55, 24, 25, 26, 27, 28, 29, 62, 63] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 64, 65, 66, 67]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 265) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/265: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])CC(C)C)cc1OC) `ZINC001184331525.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184331525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 71 natoms 70 natoms 69 natoms 68 names: ZINC001184331525 none CCN1CCC[C@@H]1CNC(=O)c1cc(S(=O)(=O)CC)c(NC(=O)[C@]([O-])([SiH3])CC(C)C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 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: [46, 46, 46, 46, 46, 46, 29, 46, 7, 7, 3, 7, 3, 3, 3, 3, 4, 4, 4, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 29, 29, 7, 3, 8, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7] 50 rigid atoms, others: [59, 60, 61, 56, 58, 57, 22, 55, 24, 25, 26, 27, 28, 29, 62, 63] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 64, 65, 66, 67]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184331525 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331525 Building ZINC001184331974 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331974' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331974 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184331974 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331974/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331974 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 266) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/266 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/266' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N[C@H](C(=O)NCCOCCOCCOCc1ccccc1)C(C)C) `ZINC001184331974.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184331974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 73 natoms 72 natoms 71 natoms 70 names: ZINC001184331974 none CC(C)C[C@@]([O-])([SiH3])C(=O)N[C@H](C(=O)NCCOCCOCCOCc1ccccc1)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.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 6, 4, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 2, 2, 2, 6, 6, 9, 17, 17, 21, 25, 25, 29, 50, 50, 50, 50, 50, 50, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 17, 17, 17, 17, 25, 25, 25, 25, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331974 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331974/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331974 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 267) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/267 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/267' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N[C@H](C(=O)NCCOCCOCCOCc1ccccc1)C(C)C) `ZINC001184331974.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184331974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331974/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 73 natoms 72 natoms 71 natoms 70 names: ZINC001184331974 none CC(C)C[C@]([O-])([SiH3])C(=O)N[C@H](C(=O)NCCOCCOCCOCc1ccccc1)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.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 6, 4, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 2, 4, 4, 4, 9, 9, 15, 19, 19, 23, 27, 27, 28, 50, 50, 50, 50, 50, 50, 2, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 9, 9, 9, 9, 19, 19, 19, 19, 27, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 33, 40, 41, 42, 39, 2, 8, 3, 9, 7, 4, 6, 5] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 223 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331974 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184331974 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331974/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331974/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331974 Building ZINC001184331974 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331974' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331974 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184331974 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331974/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331974 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 266) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC(C)C[C@@]([O-])([SiH3])C(=O)N[C@H](C(=O)NCCOCCOCCOCc1ccccc1)C(C)C) `ZINC001184331974.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184331974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 73 natoms 72 natoms 71 natoms 70 names: ZINC001184331974 none CC(C)C[C@@]([O-])([SiH3])C(=O)N[C@H](C(=O)NCCOCCOCCOCc1ccccc1)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.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 6, 4, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 2, 2, 2, 6, 6, 9, 17, 17, 21, 25, 25, 29, 50, 50, 50, 50, 50, 50, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 17, 17, 17, 17, 25, 25, 25, 25, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331974 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331974/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331974 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 267) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC(C)C[C@]([O-])([SiH3])C(=O)N[C@H](C(=O)NCCOCCOCCOCc1ccccc1)C(C)C) `ZINC001184331974.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184331974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331974/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 73 natoms 72 natoms 71 natoms 70 names: ZINC001184331974 none CC(C)C[C@]([O-])([SiH3])C(=O)N[C@H](C(=O)NCCOCCOCCOCc1ccccc1)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.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 6, 4, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 2, 4, 4, 4, 9, 9, 15, 19, 19, 23, 27, 27, 28, 50, 50, 50, 50, 50, 50, 2, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 9, 9, 9, 9, 19, 19, 19, 19, 27, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 33, 40, 41, 42, 39, 2, 8, 3, 9, 7, 4, 6, 5] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 223 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331974 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184331974 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331974/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331974/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184331974 Building ZINC001184332037 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184332037' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184332037 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184332037 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184332037/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184332037 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 268) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/268 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/268' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@@H](Cc1c[nH]c2ccccc12)C(N)=O) `ZINC001184332037.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184332037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184332037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001184332037 none CC(C)C[C@@]([O-])([SiH3])C(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@@H](Cc1c[nH]c2ccccc12)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 7, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8, 8, 8, 8, 4, 8, 8, 8, 18, 18, 37, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 37, 37, 49, 49, 49, 49, 49, 31, 31] 50 rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 8, 9, 7, 6, 5] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184332037 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184332037/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184332037 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 269) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/269 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/269' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@@H](Cc1c[nH]c2ccccc12)C(N)=O) `ZINC001184332037.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184332037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184332037/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001184332037 none CC(C)C[C@]([O-])([SiH3])C(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@@H](Cc1c[nH]c2ccccc12)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 7, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 10, 10, 10, 10, 4, 8, 8, 8, 15, 15, 32, 47, 47, 47, 47, 47, 47, 47, 47, 47, 15, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 8, 32, 32, 47, 47, 47, 47, 47, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 8, 9, 7, 6, 5] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 255 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184332037 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184332037 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184332037/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184332037/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184332037 Building ZINC001184332037 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184332037' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184332037 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184332037 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184332037/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184332037 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 268) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC(C)C[C@@]([O-])([SiH3])C(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@@H](Cc1c[nH]c2ccccc12)C(N)=O) `ZINC001184332037.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184332037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184332037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001184332037 none CC(C)C[C@@]([O-])([SiH3])C(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@@H](Cc1c[nH]c2ccccc12)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 7, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8, 8, 8, 8, 4, 8, 8, 8, 18, 18, 37, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 37, 37, 49, 49, 49, 49, 49, 31, 31] 50 rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 8, 9, 7, 6, 5] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184332037 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184332037/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184332037 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 269) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC(C)C[C@]([O-])([SiH3])C(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@@H](Cc1c[nH]c2ccccc12)C(N)=O) `ZINC001184332037.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184332037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184332037/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001184332037 none CC(C)C[C@]([O-])([SiH3])C(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@@H](Cc1c[nH]c2ccccc12)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 7, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 10, 10, 10, 10, 4, 8, 8, 8, 15, 15, 32, 47, 47, 47, 47, 47, 47, 47, 47, 47, 15, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 8, 32, 32, 47, 47, 47, 47, 47, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 8, 9, 7, 6, 5] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 255 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184332037 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184332037 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184332037/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184332037/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184332037 Building ZINC001184478554 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478554' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478554 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184478554 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478554/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478554 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 270) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/270 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/270' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1snc(C(N)=O)c1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001184478554 none CCOC(=O)c1snc(C(N)=O)c1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'N.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 14, 8, 1, 1, 8, 11, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 6, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 23, 23, 14, 23, 14, 14, 14, 14, 14, 16, 16, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 28, 28, 28, 28, 28, 16, 16, 4, 5, 5, 5, 5] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 89 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478554 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478554/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478554 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 271) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/271 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/271' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1snc(C(N)=O)c1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001184478554 none CCOC(=O)c1snc(C(N)=O)c1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'N.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 14, 8, 1, 1, 8, 11, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 6, 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: [29, 24, 24, 15, 24, 15, 15, 15, 15, 15, 17, 17, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 29, 17, 17, 4, 5, 5, 5, 5] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 91 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478554 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184478554 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478554/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478554/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478554 Building ZINC001184478554 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478554' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478554 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184478554 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478554/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478554 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 270) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCOC(=O)c1snc(C(N)=O)c1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001184478554 none CCOC(=O)c1snc(C(N)=O)c1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'N.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 14, 8, 1, 1, 8, 11, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 6, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 23, 23, 14, 23, 14, 14, 14, 14, 14, 16, 16, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 28, 28, 28, 28, 28, 16, 16, 4, 5, 5, 5, 5] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 89 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478554 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478554/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478554 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 271) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCOC(=O)c1snc(C(N)=O)c1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001184478554 none CCOC(=O)c1snc(C(N)=O)c1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'N.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 14, 8, 1, 1, 8, 11, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 6, 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: [29, 24, 24, 15, 24, 15, 15, 15, 15, 15, 17, 17, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 29, 17, 17, 4, 5, 5, 5, 5] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 91 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478554 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184478554 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478554/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478554/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478554 Building ZINC001184478590 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478590' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478590 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184478590 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478590/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478590 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 272) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/272 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/272' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1CC1)[C@@H]1C[C@@H]2[C@@H](CCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)O1) `ZINC001184478590.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184478590 none O=C(NCC1CC1)[C@@H]1C[C@@H]2[C@@H](CCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [20, 5, 20, 20, 31, 31, 31, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 20, 31, 31, 31, 31, 31, 31, 31, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478590 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478590/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478590 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 273) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/273 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/273' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1CC1)[C@@H]1C[C@@H]2[C@@H](CCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)O1) `ZINC001184478590.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478590/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184478590 none O=C(NCC1CC1)[C@@H]1C[C@@H]2[C@@H](CCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [21, 7, 21, 21, 32, 33, 33, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 21, 32, 32, 33, 33, 33, 33, 33, 7, 7, 7, 7, 7, 7, 4, 4, 4, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478590 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184478590 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478590/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478590/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478590 Building ZINC001184478590 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478590' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478590 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184478590 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478590/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478590 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 272) grep: /scratch/xiaobo/418326/xbt-8058088.46/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(NCC1CC1)[C@@H]1C[C@@H]2[C@@H](CCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)O1) `ZINC001184478590.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184478590 none O=C(NCC1CC1)[C@@H]1C[C@@H]2[C@@H](CCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [20, 5, 20, 20, 31, 31, 31, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 20, 31, 31, 31, 31, 31, 31, 31, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478590 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478590/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478590 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 273) grep: /scratch/xiaobo/418326/xbt-8058088.46/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(NCC1CC1)[C@@H]1C[C@@H]2[C@@H](CCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)O1) `ZINC001184478590.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478590/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184478590 none O=C(NCC1CC1)[C@@H]1C[C@@H]2[C@@H](CCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 7, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [21, 7, 21, 21, 32, 33, 33, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 21, 32, 32, 33, 33, 33, 33, 33, 7, 7, 7, 7, 7, 7, 4, 4, 4, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478590 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184478590 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478590/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478590/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478590 Building ZINC001184478611 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478611' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478611 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184478611 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478611/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478611 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 274) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/274 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/274' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)CN(c1cncnc1)C(=O)CO2)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478611.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184478611 none O=C(N1CCC2(CC1)CN(c1cncnc1)C(=O)CO2)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 8, 1, 1, 8, 1, 8, 1, 1, 11, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 6, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 20, 20, 20, 20, 19, 20, 20, 20, 25, 25, 24, 25, 25, 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, 25, 25, 25, 20, 20, 6, 6, 6, 6] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478611 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478611/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478611 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 275) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/275 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/275' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)CN(c1cncnc1)C(=O)CO2)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478611.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478611/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184478611 none O=C(N1CCC2(CC1)CN(c1cncnc1)C(=O)CO2)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 8, 1, 1, 8, 1, 8, 1, 1, 11, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 6, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 9, 18, 18, 18, 18, 18, 18, 18, 18, 24, 24, 23, 24, 24, 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, 24, 21, 24, 18, 18, 6, 6, 6, 6] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 53 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478611 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184478611 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478611/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478611/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478611 Building ZINC001184478611 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478611' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478611 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184478611 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478611/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478611 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 274) grep: /scratch/xiaobo/418326/xbt-8058088.46/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(N1CCC2(CC1)CN(c1cncnc1)C(=O)CO2)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478611.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184478611 none O=C(N1CCC2(CC1)CN(c1cncnc1)C(=O)CO2)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 8, 1, 1, 8, 1, 8, 1, 1, 11, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 6, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 20, 20, 20, 20, 19, 20, 20, 20, 25, 25, 24, 25, 25, 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, 25, 25, 25, 20, 20, 6, 6, 6, 6] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478611 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478611/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478611 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 275) grep: /scratch/xiaobo/418326/xbt-8058088.46/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(N1CCC2(CC1)CN(c1cncnc1)C(=O)CO2)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478611.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478611/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184478611 none O=C(N1CCC2(CC1)CN(c1cncnc1)C(=O)CO2)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 8, 1, 1, 8, 1, 8, 1, 1, 11, 5, 12, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 6, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 9, 18, 18, 18, 18, 18, 18, 18, 18, 24, 24, 23, 24, 24, 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, 24, 21, 24, 18, 18, 6, 6, 6, 6] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 53 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478611 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184478611 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478611/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478611/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478611 Building ZINC001184478673 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478673' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478673 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184478673 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478673/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478673 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 276) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/276 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/276' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CN1CC[C@@]2(CCCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C2)C1=O) `ZINC001184478673.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184478673 none CN(C)C(=O)CN1CC[C@@]2(CCCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 27, 8, 8, 8, 8, 8, 8, 8, 8, 6, 2, 7, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 27, 27, 27, 27, 27, 27, 21, 21, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 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]) total number of confs: 106 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478673 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478673/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478673 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 277) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/277 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/277' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CN1CC[C@@]2(CCCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C2)C1=O) `ZINC001184478673.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478673/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184478673 none CN(C)C(=O)CN1CC[C@@]2(CCCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 19, 26, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 26, 26, 26, 26, 26, 26, 19, 19, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 5, 5] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 100 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478673 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184478673 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478673/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478673/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478673 Building ZINC001184478673 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478673' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478673 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184478673 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478673/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478673 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 276) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CN(C)C(=O)CN1CC[C@@]2(CCCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C2)C1=O) `ZINC001184478673.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184478673 none CN(C)C(=O)CN1CC[C@@]2(CCCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 27, 8, 8, 8, 8, 8, 8, 8, 8, 6, 2, 7, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 27, 27, 27, 27, 27, 27, 21, 21, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 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]) total number of confs: 106 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478673 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478673/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478673 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 277) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CN(C)C(=O)CN1CC[C@@]2(CCCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C2)C1=O) `ZINC001184478673.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478673/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184478673 none CN(C)C(=O)CN1CC[C@@]2(CCCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 19, 26, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 26, 26, 26, 26, 26, 26, 19, 19, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 5, 5] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 100 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478673 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184478673 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478673/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478673/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478673 Building ZINC001184478679 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478679' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478679 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184478679 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478679/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478679 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 278) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/278 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/278' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CN1CC[C@]2(CCCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C2)C1=O) `ZINC001184478679.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478679/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184478679 none CN(C)C(=O)CN1CC[C@]2(CCCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 22, 30, 7, 7, 7, 7, 7, 7, 7, 7, 5, 2, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 30, 30, 30, 30, 30, 30, 22, 22, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 5, 5, 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]) total number of confs: 110 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478679 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478679/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478679 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 279) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/279 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/279' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CN1CC[C@]2(CCCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C2)C1=O) `ZINC001184478679.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478679/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184478679 none CN(C)C(=O)CN1CC[C@]2(CCCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 29, 9, 9, 9, 9, 9, 9, 9, 9, 6, 2, 8, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 29, 29, 29, 29, 29, 29, 25, 25, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 4, 4, 4, 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]) total number of confs: 114 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478679 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184478679 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478679/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478679/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478679 Building ZINC001184478679 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478679' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478679 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184478679 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478679/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478679 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 278) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CN(C)C(=O)CN1CC[C@]2(CCCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C2)C1=O) `ZINC001184478679.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478679/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184478679 none CN(C)C(=O)CN1CC[C@]2(CCCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 22, 30, 7, 7, 7, 7, 7, 7, 7, 7, 5, 2, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 30, 30, 30, 30, 30, 30, 22, 22, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 5, 5, 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]) total number of confs: 110 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478679 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478679/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478679 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 279) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CN(C)C(=O)CN1CC[C@]2(CCCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C2)C1=O) `ZINC001184478679.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478679/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184478679 none CN(C)C(=O)CN1CC[C@]2(CCCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 29, 9, 9, 9, 9, 9, 9, 9, 9, 6, 2, 8, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 29, 29, 29, 29, 29, 29, 25, 25, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 4, 4, 4, 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]) total number of confs: 114 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478679 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184478679 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478679/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478679/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478679 Building ZINC001184478817 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478817' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478817 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184478817 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478817/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478817 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 280) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/280 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/280' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(OC)nc(CN2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)n1) `ZINC001184478817.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184478817 none COc1cc(OC)nc(CN2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'N.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 8, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [29, 29, 29, 15, 29, 29, 29, 29, 15, 7, 7, 7, 7, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 29, 29, 29, 29, 15, 29, 29, 29, 15, 15, 7, 7, 7, 7, 4, 4, 4, 4, 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, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478817 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478817/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478817 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 281) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/281 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/281' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(OC)nc(CN2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)n1) `ZINC001184478817.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478817/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184478817 none COc1cc(OC)nc(CN2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'N.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 8, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 31, 31, 14, 31, 31, 31, 31, 14, 6, 6, 6, 6, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 31, 31, 31, 31, 14, 31, 31, 31, 14, 14, 6, 6, 6, 6, 4, 4, 4, 4, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 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/418326/xbt-8058088.46/working/building/ZINC001184478817 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184478817 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478817/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478817/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478817 Building ZINC001184478817 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478817' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478817 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184478817 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478817/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478817 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 280) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(OC)nc(CN2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)n1) `ZINC001184478817.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184478817 none COc1cc(OC)nc(CN2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'N.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 8, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [29, 29, 29, 15, 29, 29, 29, 29, 15, 7, 7, 7, 7, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 29, 29, 29, 29, 15, 29, 29, 29, 15, 15, 7, 7, 7, 7, 4, 4, 4, 4, 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, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478817 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478817/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478817 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 281) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(OC)nc(CN2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)n1) `ZINC001184478817.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478817/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184478817 none COc1cc(OC)nc(CN2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'N.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 8, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 31, 31, 14, 31, 31, 31, 31, 14, 6, 6, 6, 6, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 31, 31, 31, 31, 14, 31, 31, 31, 14, 14, 6, 6, 6, 6, 4, 4, 4, 4, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 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/418326/xbt-8058088.46/working/building/ZINC001184478817 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184478817 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478817/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478817/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184478817 Building ZINC001184479401 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479401' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479401 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479401 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479401/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479401 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 282) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/282 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/282' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H]1Cn2nnc(c3cnn(C)c3)c2CN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479401.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001184479401 none COC[C@@H]1Cn2nnc(c3cnn(C)c3)c2CN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 8, 8, 1, 1, 1, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 13, 4, 4, 4, 4, 4, 4, 4, 4, 4, 23, 23, 23, 23, 23, 4, 4, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 13, 13, 4, 4, 23, 23, 23, 23, 23, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479401 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479401/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479401 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 283) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/283 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/283' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H]1Cn2nnc(c3cnn(C)c3)c2CN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479401.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479401/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001184479401 none COC[C@@H]1Cn2nnc(c3cnn(C)c3)c2CN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 8, 8, 1, 1, 1, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19, 19, 19, 19, 4, 4, 3, 2, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 14, 11, 11, 4, 4, 19, 19, 19, 19, 19, 4, 4, 5, 5, 5, 5] 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: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479401 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184479401 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479401/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479401/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479401 Building ZINC001184479401 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479401' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479401 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479401 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479401/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479401 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 282) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COC[C@@H]1Cn2nnc(c3cnn(C)c3)c2CN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479401.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001184479401 none COC[C@@H]1Cn2nnc(c3cnn(C)c3)c2CN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 8, 8, 1, 1, 1, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 13, 4, 4, 4, 4, 4, 4, 4, 4, 4, 23, 23, 23, 23, 23, 4, 4, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 13, 13, 4, 4, 23, 23, 23, 23, 23, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479401 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479401/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479401 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 283) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COC[C@@H]1Cn2nnc(c3cnn(C)c3)c2CN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479401.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479401/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001184479401 none COC[C@@H]1Cn2nnc(c3cnn(C)c3)c2CN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 8, 8, 1, 1, 1, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19, 19, 19, 19, 4, 4, 3, 2, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 14, 11, 11, 4, 4, 19, 19, 19, 19, 19, 4, 4, 5, 5, 5, 5] 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: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479401 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184479401 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479401/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479401/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479401 Building ZINC001184479403 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479403' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479403 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479403 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479403/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479403 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 284) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/284 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/284' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H]1Cn2nnc(c3cnn(C)c3)c2CN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479403.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001184479403 none COC[C@H]1Cn2nnc(c3cnn(C)c3)c2CN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 8, 8, 1, 1, 1, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19, 19, 19, 19, 4, 4, 3, 2, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 11, 11, 4, 4, 19, 19, 19, 19, 19, 4, 4, 5, 5, 5, 5] 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: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479403 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479403/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479403 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 285) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/285 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/285' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H]1Cn2nnc(c3cnn(C)c3)c2CN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479403.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479403/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001184479403 none COC[C@H]1Cn2nnc(c3cnn(C)c3)c2CN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 8, 8, 1, 1, 1, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 4, 4, 4, 4, 4, 23, 23, 23, 23, 23, 4, 4, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 12, 12, 4, 4, 23, 23, 23, 23, 23, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479403 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184479403 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479403/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479403/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479403 Building ZINC001184479403 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479403' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479403 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479403 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479403/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479403 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 284) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COC[C@H]1Cn2nnc(c3cnn(C)c3)c2CN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479403.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001184479403 none COC[C@H]1Cn2nnc(c3cnn(C)c3)c2CN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 8, 8, 1, 1, 1, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19, 19, 19, 19, 4, 4, 3, 2, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 11, 11, 4, 4, 19, 19, 19, 19, 19, 4, 4, 5, 5, 5, 5] 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: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479403 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479403/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479403 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 285) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COC[C@H]1Cn2nnc(c3cnn(C)c3)c2CN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479403.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479403/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001184479403 none COC[C@H]1Cn2nnc(c3cnn(C)c3)c2CN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 8, 8, 1, 1, 1, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 4, 4, 4, 4, 4, 23, 23, 23, 23, 23, 4, 4, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 12, 12, 4, 4, 23, 23, 23, 23, 23, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479403 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184479403 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479403/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479403/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479403 Building ZINC001184479478 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479478' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479478 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479478 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479478/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479478 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 286) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/286 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/286' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)COCc1noc2c1CN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184479478.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184479478 none CN(C)C(=O)COCc1noc2c1CN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 12, 5, 1, 8, 12, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 41, 33, 17, 4, 4, 4, 4, 4, 4, 4, 2, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 41, 41, 41, 41, 41, 41, 40, 40, 17, 17, 4, 4, 4, 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, 49, 50, 51]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479478 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479478/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479478 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 287) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/287 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/287' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)COCc1noc2c1CN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184479478.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479478/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184479478 none CN(C)C(=O)COCc1noc2c1CN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 12, 5, 1, 8, 12, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 34, 17, 4, 4, 4, 4, 4, 4, 4, 2, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 41, 41, 41, 41, 41, 41, 41, 41, 17, 17, 4, 4, 4, 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, 49, 50, 51]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479478 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184479478 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479478/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479478/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479478 Building ZINC001184479478 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479478' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479478 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479478 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479478/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479478 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 286) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CN(C)C(=O)COCc1noc2c1CN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184479478.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184479478 none CN(C)C(=O)COCc1noc2c1CN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 12, 5, 1, 8, 12, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 41, 33, 17, 4, 4, 4, 4, 4, 4, 4, 2, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 41, 41, 41, 41, 41, 41, 40, 40, 17, 17, 4, 4, 4, 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, 49, 50, 51]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479478 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479478/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479478 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 287) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CN(C)C(=O)COCc1noc2c1CN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184479478.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479478/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184479478 none CN(C)C(=O)COCc1noc2c1CN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 12, 5, 1, 8, 12, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 34, 17, 4, 4, 4, 4, 4, 4, 4, 2, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 41, 41, 41, 41, 41, 41, 41, 41, 17, 17, 4, 4, 4, 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, 49, 50, 51]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479478 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184479478 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479478/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479478/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479478 Building ZINC001184479940 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479940' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479940 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479940 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479940/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479940 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 288) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/288 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/288' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cnccn1)[C@H]1COC[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@H]21) `ZINC001184479940.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479940/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184479940 none O=C(Nc1cnccn1)[C@H]1COC[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@H]21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 1, 1, 8, 5, 7, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 3, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 7, 23, 23, 25, 25, 25, 25, 25, 7, 7, 7, 7, 7, 7, 7, 7, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 23, 25, 25, 25, 7, 7, 7, 7, 7, 7, 4, 4, 4, 4, 7, 7] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 64 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479940 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479940/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479940 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 289) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/289 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/289' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cnccn1)[C@H]1COC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@H]21) `ZINC001184479940.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479940/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184479940 none O=C(Nc1cnccn1)[C@H]1COC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@H]21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 1, 1, 8, 5, 7, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 3, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 23, 23, 23, 23, 23, 23, 23, 9, 9, 9, 9, 9, 9, 9, 9, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 23, 23, 23, 23, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 9, 9] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 57 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479940 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184479940 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479940/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479940/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479940 Building ZINC001184479940 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479940' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479940 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479940 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479940/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479940 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 288) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/288: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cnccn1)[C@H]1COC[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@H]21) `ZINC001184479940.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479940/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184479940 none O=C(Nc1cnccn1)[C@H]1COC[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@H]21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 1, 1, 8, 5, 7, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 3, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 7, 23, 23, 25, 25, 25, 25, 25, 7, 7, 7, 7, 7, 7, 7, 7, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 23, 25, 25, 25, 7, 7, 7, 7, 7, 7, 4, 4, 4, 4, 7, 7] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 64 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479940 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479940/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479940 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 289) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/289: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cnccn1)[C@H]1COC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@H]21) `ZINC001184479940.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479940/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184479940 none O=C(Nc1cnccn1)[C@H]1COC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@H]21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 1, 1, 8, 5, 7, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 3, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 23, 23, 23, 23, 23, 23, 23, 9, 9, 9, 9, 9, 9, 9, 9, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 23, 23, 23, 23, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 9, 9] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 57 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479940 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184479940 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479940/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479940/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479940 Building ZINC001184479961 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479961' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479961 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479961 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479961/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479961 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 290) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/290 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/290' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)COC[C@H]1CC[C@@H]2[C@@H](CCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)O1) `ZINC001184479961.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184479961 none CN(C)C(=O)COC[C@H]1CC[C@@H]2[C@@H](CCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 12, 5, 5, 7, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 39, 24, 18, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 39, 39, 39, 39, 39, 39, 34, 34, 18, 18, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 3, 3] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479961 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479961/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479961 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 291) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/291 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/291' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)COC[C@H]1CC[C@@H]2[C@@H](CCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)O1) `ZINC001184479961.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479961/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184479961 none CN(C)C(=O)COC[C@H]1CC[C@@H]2[C@@H](CCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 12, 5, 5, 7, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 35, 20, 14, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 35, 35, 35, 35, 35, 35, 33, 33, 14, 14, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 3, 3] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479961 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184479961 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479961/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479961/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479961 Building ZINC001184479961 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479961' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479961 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479961 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479961/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479961 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 290) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/290: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)COC[C@H]1CC[C@@H]2[C@@H](CCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)O1) `ZINC001184479961.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184479961 none CN(C)C(=O)COC[C@H]1CC[C@@H]2[C@@H](CCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 12, 5, 5, 7, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 39, 24, 18, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 39, 39, 39, 39, 39, 39, 34, 34, 18, 18, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 3, 3] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479961 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479961/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479961 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 291) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/291: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)COC[C@H]1CC[C@@H]2[C@@H](CCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)O1) `ZINC001184479961.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479961/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184479961 none CN(C)C(=O)COC[C@H]1CC[C@@H]2[C@@H](CCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 12, 5, 5, 7, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 35, 20, 14, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 35, 35, 35, 35, 35, 35, 33, 33, 14, 14, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 3, 3] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479961 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184479961 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479961/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479961/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479961 Building ZINC001184479997 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184479997 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 292) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/292 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/292' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCC12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184479997.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184479997 none CNC(=O)CN1CCCC12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 32, 24, 24, 24, 24, 24, 24, 24, 24, 8, 1, 13, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 32, 32, 32, 32, 29, 29, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 6, 6, 6, 6, 24, 24, 24, 24] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 293) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/293 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/293' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCC12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184479997.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184479997 none CNC(=O)CN1CCCC12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 32, 24, 24, 24, 24, 24, 24, 24, 24, 8, 1, 13, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 32, 32, 32, 32, 29, 29, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 6, 6, 6, 6, 24, 24, 24, 24] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 294) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/294 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/294' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCC12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184479997.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184479997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184479997 none CNC(=O)CN1CCCC12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 30, 21, 21, 21, 21, 21, 21, 21, 21, 8, 1, 12, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 30, 30, 30, 30, 26, 26, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 21, 21, 21, 21] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 295) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/295 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/295' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCC12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184479997.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184479997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184479997 none CNC(=O)CN1CCCC12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 30, 21, 21, 21, 21, 21, 21, 21, 21, 8, 1, 12, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 30, 30, 30, 30, 26, 26, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 21, 21, 21, 21] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184479997 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997 Building ZINC001184479997 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184479997 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 292) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CNC(=O)CN1CCCC12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184479997.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184479997 none CNC(=O)CN1CCCC12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 32, 24, 24, 24, 24, 24, 24, 24, 24, 8, 1, 13, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 32, 32, 32, 32, 29, 29, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 6, 6, 6, 6, 24, 24, 24, 24] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 293) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CNC(=O)CN1CCCC12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184479997.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184479997 none CNC(=O)CN1CCCC12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 32, 24, 24, 24, 24, 24, 24, 24, 24, 8, 1, 13, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 32, 32, 32, 32, 29, 29, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 6, 6, 6, 6, 24, 24, 24, 24] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 294) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/294: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCC12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184479997.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184479997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184479997 none CNC(=O)CN1CCCC12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 30, 21, 21, 21, 21, 21, 21, 21, 21, 8, 1, 12, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 30, 30, 30, 30, 26, 26, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 21, 21, 21, 21] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 295) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/295: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCC12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184479997.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184479997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184479997 none CNC(=O)CN1CCCC12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 30, 21, 21, 21, 21, 21, 21, 21, 21, 8, 1, 12, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 30, 30, 30, 30, 26, 26, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 21, 21, 21, 21] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184479997 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997 Building ZINC001184479997 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184479997 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 292) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CNC(=O)CN1CCCC12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184479997.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184479997 none CNC(=O)CN1CCCC12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 32, 24, 24, 24, 24, 24, 24, 24, 24, 8, 1, 13, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 32, 32, 32, 32, 29, 29, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 6, 6, 6, 6, 24, 24, 24, 24] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 293) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CNC(=O)CN1CCCC12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184479997.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184479997 none CNC(=O)CN1CCCC12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 32, 24, 24, 24, 24, 24, 24, 24, 24, 8, 1, 13, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 32, 32, 32, 32, 29, 29, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 6, 6, 6, 6, 24, 24, 24, 24] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 294) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/294: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCC12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184479997.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184479997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184479997 none CNC(=O)CN1CCCC12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 30, 21, 21, 21, 21, 21, 21, 21, 21, 8, 1, 12, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 30, 30, 30, 30, 26, 26, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 21, 21, 21, 21] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 295) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/295: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCC12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184479997.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184479997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184479997 none CNC(=O)CN1CCCC12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 30, 21, 21, 21, 21, 21, 21, 21, 21, 8, 1, 12, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 30, 30, 30, 30, 26, 26, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 21, 21, 21, 21] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184479997 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997 Building ZINC001184479997 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184479997 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 292) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CNC(=O)CN1CCCC12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184479997.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184479997 none CNC(=O)CN1CCCC12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 32, 24, 24, 24, 24, 24, 24, 24, 24, 8, 1, 13, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 32, 32, 32, 32, 29, 29, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 6, 6, 6, 6, 24, 24, 24, 24] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 293) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CNC(=O)CN1CCCC12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184479997.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184479997 none CNC(=O)CN1CCCC12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 32, 24, 24, 24, 24, 24, 24, 24, 24, 8, 1, 13, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 32, 32, 32, 32, 29, 29, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 6, 6, 6, 6, 24, 24, 24, 24] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 294) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/294: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCC12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184479997.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184479997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184479997 none CNC(=O)CN1CCCC12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 30, 21, 21, 21, 21, 21, 21, 21, 21, 8, 1, 12, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 30, 30, 30, 30, 26, 26, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 21, 21, 21, 21] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 295) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/295: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCC12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184479997.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184479997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001184479997 none CNC(=O)CN1CCCC12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 30, 21, 21, 21, 21, 21, 21, 21, 21, 8, 1, 12, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 30, 30, 30, 30, 26, 26, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 21, 21, 21, 21] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184479997 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184479997 Building ZINC001184480064 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480064' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480064 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480064 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480064/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480064 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 296) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/296 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/296' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@H]2S1(=O)=O) `ZINC001184480064.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001184480064 none CCN1C[C@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@H]2S1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 14, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 19, 19, 19, 19, 19, 19, 19, 12, 1, 13, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 19, 19, 19, 19, 19, 19, 19, 20, 20, 20, 20, 20, 19, 19, 19, 19, 19, 19, 5, 5, 5, 5, 19, 19, 19, 19] 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: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480064 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480064/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480064 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 297) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/297 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/297' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@H]2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@H]2S1(=O)=O) `ZINC001184480064.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480064/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001184480064 none CCN1C[C@H]2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@H]2S1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 14, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 14, 1, 15, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 5, 5, 5, 5, 25, 25, 25, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480064 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184480064 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480064/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480064/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480064 Building ZINC001184480064 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480064' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480064 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480064 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480064/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480064 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 296) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCN1C[C@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@H]2S1(=O)=O) `ZINC001184480064.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001184480064 none CCN1C[C@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@H]2S1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 14, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 19, 19, 19, 19, 19, 19, 19, 12, 1, 13, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 19, 19, 19, 19, 19, 19, 19, 20, 20, 20, 20, 20, 19, 19, 19, 19, 19, 19, 5, 5, 5, 5, 19, 19, 19, 19] 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: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480064 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480064/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480064 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 297) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCN1C[C@H]2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@H]2S1(=O)=O) `ZINC001184480064.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480064/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001184480064 none CCN1C[C@H]2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@H]2S1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 14, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 14, 1, 15, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 5, 5, 5, 5, 25, 25, 25, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480064 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184480064 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480064/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480064/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480064 Building ZINC001184480091 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480091' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480091 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480091 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480091/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480091 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 298) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/298 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/298' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(=O)N2CC[C@@H]3[C@@H]2CCN3C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cn1) `ZINC001184480091.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480091.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480091/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184480091 none Cn1cc(C(=O)N2CC[C@@H]3[C@@H]2CCN3C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 11, 3, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 24, 24, 24, 24, 24, 24, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 24] 50 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480091 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480091/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480091 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 299) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/299 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/299' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(=O)N2CC[C@@H]3[C@@H]2CCN3C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cn1) `ZINC001184480091.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480091.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480091/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184480091 none Cn1cc(C(=O)N2CC[C@@H]3[C@@H]2CCN3C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 13, 5, 13, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 24, 24, 24, 24, 24, 24, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 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]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480091 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184480091 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480091/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480091/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480091 Building ZINC001184480091 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480091' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480091 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480091 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480091/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480091 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 298) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(C(=O)N2CC[C@@H]3[C@@H]2CCN3C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cn1) `ZINC001184480091.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480091.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480091/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184480091 none Cn1cc(C(=O)N2CC[C@@H]3[C@@H]2CCN3C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 11, 3, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 24, 24, 24, 24, 24, 24, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 24] 50 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480091 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480091/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480091 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 299) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(C(=O)N2CC[C@@H]3[C@@H]2CCN3C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cn1) `ZINC001184480091.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480091.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480091/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184480091 none Cn1cc(C(=O)N2CC[C@@H]3[C@@H]2CCN3C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 13, 5, 13, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 24, 24, 24, 24, 24, 24, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 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]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480091 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184480091 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480091/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480091/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480091 Building ZINC001184480142 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480142' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480142 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480142 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480142/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480142 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 300) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/300 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/300' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CO[C@@H]1COC2(C1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184480142.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184480142 none CNC(=O)CO[C@@H]1COC2(C1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 7, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 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, 4, 7, 6, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 29, 29, 29, 29, 29, 29, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 4, 4, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480142 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480142/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480142 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 301) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/301 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/301' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CO[C@@H]1COC2(C1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184480142.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480142/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184480142 none CNC(=O)CO[C@@H]1COC2(C1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 7, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 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, 4, 7, 6, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 19, 9, 9, 9, 9, 9, 9, 9, 9, 7, 6, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 33, 33, 33, 33, 33, 33, 9, 9, 9, 9, 9, 9, 9, 9, 4, 4, 4, 4, 9, 9, 9, 9] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 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/418326/xbt-8058088.46/working/building/ZINC001184480142 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184480142 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480142/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480142/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480142 Building ZINC001184480142 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480142' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480142 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480142 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480142/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480142 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 300) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/300: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CO[C@@H]1COC2(C1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184480142.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184480142 none CNC(=O)CO[C@@H]1COC2(C1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 7, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 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, 4, 7, 6, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 29, 29, 29, 29, 29, 29, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 4, 4, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480142 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480142/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480142 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 301) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/301: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CO[C@@H]1COC2(C1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184480142.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480142/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184480142 none CNC(=O)CO[C@@H]1COC2(C1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 7, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 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, 4, 7, 6, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 19, 9, 9, 9, 9, 9, 9, 9, 9, 7, 6, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 33, 33, 33, 33, 33, 33, 9, 9, 9, 9, 9, 9, 9, 9, 4, 4, 4, 4, 9, 9, 9, 9] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 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/418326/xbt-8058088.46/working/building/ZINC001184480142 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184480142 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480142/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480142/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480142 Building ZINC001184480143 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480143' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480143 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480143 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480143/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480143 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 302) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/302 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/302' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CO[C@H]1COC2(C1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184480143.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184480143 none CNC(=O)CO[C@H]1COC2(C1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 7, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 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, 4, 7, 6, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 2, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 31, 31, 31, 31, 31, 31, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 4, 7, 7, 7, 7] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480143 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480143/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480143 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 303) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/303 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/303' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CO[C@H]1COC2(C1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184480143.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480143/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184480143 none CNC(=O)CO[C@H]1COC2(C1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 7, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 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, 4, 7, 6, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 35, 35, 35, 35, 35, 35, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 4, 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480143 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184480143 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480143/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480143/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480143 Building ZINC001184480143 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480143' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480143 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480143 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480143/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480143 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 302) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CNC(=O)CO[C@H]1COC2(C1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184480143.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184480143 none CNC(=O)CO[C@H]1COC2(C1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 7, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 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, 4, 7, 6, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 2, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 31, 31, 31, 31, 31, 31, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 4, 7, 7, 7, 7] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480143 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480143/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480143 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 303) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CNC(=O)CO[C@H]1COC2(C1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184480143.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480143/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184480143 none CNC(=O)CO[C@H]1COC2(C1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 7, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 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, 4, 7, 6, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 35, 35, 35, 35, 35, 35, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 4, 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480143 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184480143 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480143/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480143/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480143 Building ZINC001184480389 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480389' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480389 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480389 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480389/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480389 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 304) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/304 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/304' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(N2C(=O)C[C@@H]3[C@@H]2CCN3C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cn1) `ZINC001184480389.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184480389 none Cn1cc(N2C(=O)C[C@@H]3[C@@H]2CCN3C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 11, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 19, 19, 19, 19, 19, 19, 9, 9, 9, 9, 9, 9, 7, 7, 7, 7, 19] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 41 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480389 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480389/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480389 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 305) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/305 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/305' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(N2C(=O)C[C@@H]3[C@@H]2CCN3C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cn1) `ZINC001184480389.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480389/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184480389 none Cn1cc(N2C(=O)C[C@@H]3[C@@H]2CCN3C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 11, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 16, 16, 16, 16, 16, 16, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 16] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480389 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184480389 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480389/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480389/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480389 Building ZINC001184480389 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480389' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480389 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480389 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480389/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480389 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 304) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(N2C(=O)C[C@@H]3[C@@H]2CCN3C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cn1) `ZINC001184480389.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184480389 none Cn1cc(N2C(=O)C[C@@H]3[C@@H]2CCN3C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 11, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 19, 19, 19, 19, 19, 19, 9, 9, 9, 9, 9, 9, 7, 7, 7, 7, 19] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 41 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480389 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480389/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480389 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 305) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(N2C(=O)C[C@@H]3[C@@H]2CCN3C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cn1) `ZINC001184480389.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480389/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184480389 none Cn1cc(N2C(=O)C[C@@H]3[C@@H]2CCN3C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 11, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 16, 16, 16, 16, 16, 16, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 16] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480389 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184480389 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480389/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480389/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480389 Building ZINC001184480414 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184480414 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 306) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/306 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/306' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(N2CCO[C@H]3CN(C(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)C[C@H]32)nn1) `ZINC001184480414.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184480414 none Cc1ccc(N2CCO[C@H]3CN(C(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)C[C@H]32)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [20, 20, 20, 20, 12, 12, 12, 12, 12, 12, 12, 12, 3, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 20, 20, 20, 20, 20, 20, 20, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5, 12, 12] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 307) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/307 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/307' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(N2CCO[C@H]3CN(C(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)C[C@H]32)nn1) `ZINC001184480414.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184480414 none Cc1ccc(N2CCO[C@H]3CN(C(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)C[C@H]32)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [20, 20, 20, 20, 12, 12, 12, 12, 12, 12, 12, 12, 3, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 20, 20, 20, 20, 20, 20, 20, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5, 12, 12] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 308) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/308 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/308' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(N2CCO[C@H]3CN(C(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)C[C@H]32)nn1) `ZINC001184480414.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184480414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184480414 none Cc1ccc(N2CCO[C@H]3CN(C(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)C[C@H]32)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [33, 33, 33, 33, 19, 19, 19, 19, 19, 19, 19, 18, 3, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 19, 19, 19, 33, 33, 33, 33, 33, 33, 33, 19, 19, 19, 19, 19, 19, 5, 5, 5, 5, 19, 19] 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 309) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/309 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/309' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(N2CCO[C@H]3CN(C(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)C[C@H]32)nn1) `ZINC001184480414.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184480414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184480414 none Cc1ccc(N2CCO[C@H]3CN(C(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)C[C@H]32)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [33, 33, 33, 33, 19, 19, 19, 19, 19, 19, 19, 18, 3, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 19, 19, 19, 33, 33, 33, 33, 33, 33, 33, 19, 19, 19, 19, 19, 19, 5, 5, 5, 5, 19, 19] 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184480414 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414 Building ZINC001184480414 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184480414 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 306) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1ccc(N2CCO[C@H]3CN(C(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)C[C@H]32)nn1) `ZINC001184480414.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184480414 none Cc1ccc(N2CCO[C@H]3CN(C(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)C[C@H]32)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [20, 20, 20, 20, 12, 12, 12, 12, 12, 12, 12, 12, 3, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 20, 20, 20, 20, 20, 20, 20, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5, 12, 12] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 307) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1ccc(N2CCO[C@H]3CN(C(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)C[C@H]32)nn1) `ZINC001184480414.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184480414 none Cc1ccc(N2CCO[C@H]3CN(C(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)C[C@H]32)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [20, 20, 20, 20, 12, 12, 12, 12, 12, 12, 12, 12, 3, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 20, 20, 20, 20, 20, 20, 20, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5, 12, 12] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 308) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/308: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(N2CCO[C@H]3CN(C(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)C[C@H]32)nn1) `ZINC001184480414.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184480414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184480414 none Cc1ccc(N2CCO[C@H]3CN(C(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)C[C@H]32)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [33, 33, 33, 33, 19, 19, 19, 19, 19, 19, 19, 18, 3, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 19, 19, 19, 33, 33, 33, 33, 33, 33, 33, 19, 19, 19, 19, 19, 19, 5, 5, 5, 5, 19, 19] 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 309) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/309: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(N2CCO[C@H]3CN(C(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)C[C@H]32)nn1) `ZINC001184480414.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184480414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184480414 none Cc1ccc(N2CCO[C@H]3CN(C(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)C[C@H]32)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [33, 33, 33, 33, 19, 19, 19, 19, 19, 19, 19, 18, 3, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 19, 19, 19, 33, 33, 33, 33, 33, 33, 33, 19, 19, 19, 19, 19, 19, 5, 5, 5, 5, 19, 19] 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184480414 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414 Building ZINC001184480414 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184480414 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 306) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1ccc(N2CCO[C@H]3CN(C(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)C[C@H]32)nn1) `ZINC001184480414.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184480414 none Cc1ccc(N2CCO[C@H]3CN(C(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)C[C@H]32)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [20, 20, 20, 20, 12, 12, 12, 12, 12, 12, 12, 12, 3, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 20, 20, 20, 20, 20, 20, 20, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5, 12, 12] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 307) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1ccc(N2CCO[C@H]3CN(C(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)C[C@H]32)nn1) `ZINC001184480414.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184480414 none Cc1ccc(N2CCO[C@H]3CN(C(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)C[C@H]32)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [20, 20, 20, 20, 12, 12, 12, 12, 12, 12, 12, 12, 3, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 20, 20, 20, 20, 20, 20, 20, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5, 12, 12] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 308) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/308: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(N2CCO[C@H]3CN(C(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)C[C@H]32)nn1) `ZINC001184480414.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184480414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184480414 none Cc1ccc(N2CCO[C@H]3CN(C(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)C[C@H]32)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [33, 33, 33, 33, 19, 19, 19, 19, 19, 19, 19, 18, 3, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 19, 19, 19, 33, 33, 33, 33, 33, 33, 33, 19, 19, 19, 19, 19, 19, 5, 5, 5, 5, 19, 19] 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 309) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/309: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(N2CCO[C@H]3CN(C(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)C[C@H]32)nn1) `ZINC001184480414.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184480414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184480414 none Cc1ccc(N2CCO[C@H]3CN(C(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)C[C@H]32)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [33, 33, 33, 33, 19, 19, 19, 19, 19, 19, 19, 18, 3, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 19, 19, 19, 33, 33, 33, 33, 33, 33, 33, 19, 19, 19, 19, 19, 19, 5, 5, 5, 5, 19, 19] 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184480414 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414 Building ZINC001184480414 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184480414 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 306) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1ccc(N2CCO[C@H]3CN(C(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)C[C@H]32)nn1) `ZINC001184480414.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184480414 none Cc1ccc(N2CCO[C@H]3CN(C(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)C[C@H]32)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [20, 20, 20, 20, 12, 12, 12, 12, 12, 12, 12, 12, 3, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 20, 20, 20, 20, 20, 20, 20, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5, 12, 12] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 307) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1ccc(N2CCO[C@H]3CN(C(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)C[C@H]32)nn1) `ZINC001184480414.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184480414 none Cc1ccc(N2CCO[C@H]3CN(C(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)C[C@H]32)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [20, 20, 20, 20, 12, 12, 12, 12, 12, 12, 12, 12, 3, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 20, 20, 20, 20, 20, 20, 20, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5, 12, 12] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 308) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/308: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(N2CCO[C@H]3CN(C(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)C[C@H]32)nn1) `ZINC001184480414.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184480414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184480414 none Cc1ccc(N2CCO[C@H]3CN(C(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)C[C@H]32)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [33, 33, 33, 33, 19, 19, 19, 19, 19, 19, 19, 18, 3, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 19, 19, 19, 33, 33, 33, 33, 33, 33, 33, 19, 19, 19, 19, 19, 19, 5, 5, 5, 5, 19, 19] 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 309) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/309: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(N2CCO[C@H]3CN(C(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)C[C@H]32)nn1) `ZINC001184480414.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184480414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184480414 none Cc1ccc(N2CCO[C@H]3CN(C(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)C[C@H]32)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [33, 33, 33, 33, 19, 19, 19, 19, 19, 19, 19, 18, 3, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 19, 19, 19, 33, 33, 33, 33, 33, 33, 33, 19, 19, 19, 19, 19, 19, 5, 5, 5, 5, 19, 19] 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184480414 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480414 Building ZINC001184480424 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480424' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480424 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480424 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480424/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480424 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 310) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/310 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/310' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2COC[C@H]12) `ZINC001184480424.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184480424 none Cn1cccc1C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2COC[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 12, 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, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 17, 17, 17, 8, 8, 8, 8, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 8, 8, 8, 32, 32, 32, 32, 32, 32, 17, 8, 8, 5, 5, 5, 5, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480424 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480424/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480424 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 311) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/311 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/311' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2COC[C@H]12) `ZINC001184480424.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480424/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184480424 none Cn1cccc1C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2COC[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 12, 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, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 17, 6, 6, 5, 5, 5, 5, 6, 6, 6, 6] 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]) total number of confs: 66 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480424 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184480424 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480424/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480424/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480424 Building ZINC001184480424 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480424' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480424 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480424 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480424/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480424 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 310) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cccc1C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2COC[C@H]12) `ZINC001184480424.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184480424 none Cn1cccc1C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2COC[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 12, 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, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 17, 17, 17, 8, 8, 8, 8, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 8, 8, 8, 32, 32, 32, 32, 32, 32, 17, 8, 8, 5, 5, 5, 5, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480424 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480424/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480424 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 311) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cccc1C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2COC[C@H]12) `ZINC001184480424.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480424/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184480424 none Cn1cccc1C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2COC[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 12, 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, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 17, 6, 6, 5, 5, 5, 5, 6, 6, 6, 6] 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]) total number of confs: 66 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480424 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184480424 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480424/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480424/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480424 Building ZINC001184480495 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480495' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480495 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480495 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480495/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480495 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 312) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/312 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/312' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([C@H]1COC[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@H]21)N1CCCCO1) `ZINC001184480495.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001184480495 none O=C([C@H]1COC[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@H]21)N1CCCCO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 7, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 8, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 24, 25, 25, 25, 25, 25, 8, 8, 8, 8, 8, 8, 4, 4, 4, 4, 8, 8, 25, 25, 25, 25, 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, 50, 51, 52, 53, 54]) total number of confs: 54 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480495 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480495/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480495 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 313) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/313 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/313' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([C@H]1COC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@H]21)N1CCCCO1) `ZINC001184480495.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480495/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001184480495 none O=C([C@H]1COC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@H]21)N1CCCCO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 7, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 8, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 6, 6, 5, 5, 5, 5, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21] 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: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480495 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184480495 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480495/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480495/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480495 Building ZINC001184480495 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480495' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480495 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480495 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480495/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480495 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 312) grep: /scratch/xiaobo/418326/xbt-8058088.46/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([C@H]1COC[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@H]21)N1CCCCO1) `ZINC001184480495.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001184480495 none O=C([C@H]1COC[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@H]21)N1CCCCO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 7, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 8, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 24, 25, 25, 25, 25, 25, 8, 8, 8, 8, 8, 8, 4, 4, 4, 4, 8, 8, 25, 25, 25, 25, 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, 50, 51, 52, 53, 54]) total number of confs: 54 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480495 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480495/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480495 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 313) grep: /scratch/xiaobo/418326/xbt-8058088.46/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([C@H]1COC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@H]21)N1CCCCO1) `ZINC001184480495.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480495/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001184480495 none O=C([C@H]1COC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@H]21)N1CCCCO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 7, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 8, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 6, 6, 5, 5, 5, 5, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21] 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: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480495 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184480495 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480495/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480495/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480495 Building ZINC001184480501 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480501' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480501 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480501 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480501/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480501 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 314) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/314 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/314' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCc1ncn2c1CN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CCC2) `ZINC001184480501.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184480501 none CC(=O)NCc1ncn2c1CN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 8, 1, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 20, 6, 6, 6, 6, 6, 6, 6, 3, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 24, 24, 24, 24, 20, 20, 6, 6, 6, 4, 4, 4, 4, 6, 6, 6, 6, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 90 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480501 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480501/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480501 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 315) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/315 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/315' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCc1ncn2c1CN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CCC2) `ZINC001184480501.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480501/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184480501 none CC(=O)NCc1ncn2c1CN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 8, 1, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 9, 9, 9, 9, 9, 9, 9, 3, 1, 7, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 23, 23, 23, 23, 23, 23, 9, 9, 9, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 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/418326/xbt-8058088.46/working/building/ZINC001184480501 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184480501 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480501/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480501/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480501 Building ZINC001184480501 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480501' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480501 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480501 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480501/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480501 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 314) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/314: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCc1ncn2c1CN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CCC2) `ZINC001184480501.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184480501 none CC(=O)NCc1ncn2c1CN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 8, 1, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 20, 6, 6, 6, 6, 6, 6, 6, 3, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 24, 24, 24, 24, 20, 20, 6, 6, 6, 4, 4, 4, 4, 6, 6, 6, 6, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 90 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480501 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480501/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480501 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 315) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/315: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCc1ncn2c1CN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CCC2) `ZINC001184480501.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480501/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184480501 none CC(=O)NCc1ncn2c1CN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 8, 1, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 9, 9, 9, 9, 9, 9, 9, 3, 1, 7, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 23, 23, 23, 23, 23, 23, 9, 9, 9, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 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/418326/xbt-8058088.46/working/building/ZINC001184480501 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184480501 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480501/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480501/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480501 Building ZINC001184480514 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480514' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480514 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480514 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480514/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480514 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 316) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/316 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/316' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)NC[C@H]1OC[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@@H]21) `ZINC001184480514.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184480514 none CN(C)C(=O)NC[C@H]1OC[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 7, 12, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 37, 25, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 10, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 38, 38, 38, 38, 38, 38, 37, 25, 25, 10, 10, 10, 10, 10, 10, 4, 4, 4, 4, 10, 10] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480514 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480514/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480514 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 317) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/317 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/317' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)NC[C@H]1OC[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@@H]21) `ZINC001184480514.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480514/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184480514 none CN(C)C(=O)NC[C@H]1OC[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 7, 12, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 36, 37, 36, 36, 23, 12, 12, 12, 12, 12, 12, 12, 12, 12, 9, 2, 10, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 37, 37, 37, 37, 37, 37, 36, 23, 23, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5, 12, 12] 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]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480514 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184480514 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480514/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480514/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480514 Building ZINC001184480514 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480514' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480514 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480514 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480514/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480514 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 316) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CN(C)C(=O)NC[C@H]1OC[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@@H]21) `ZINC001184480514.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184480514 none CN(C)C(=O)NC[C@H]1OC[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 7, 12, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 37, 25, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 10, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 38, 38, 38, 38, 38, 38, 37, 25, 25, 10, 10, 10, 10, 10, 10, 4, 4, 4, 4, 10, 10] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480514 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480514/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480514 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 317) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CN(C)C(=O)NC[C@H]1OC[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@@H]21) `ZINC001184480514.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480514/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184480514 none CN(C)C(=O)NC[C@H]1OC[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 7, 12, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 36, 37, 36, 36, 23, 12, 12, 12, 12, 12, 12, 12, 12, 12, 9, 2, 10, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 37, 37, 37, 37, 37, 37, 36, 23, 23, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5, 12, 12] 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]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480514 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184480514 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480514/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480514/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480514 Building ZINC001184480825 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184480825 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 318) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/318 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/318' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480825.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480825 none O=C(N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 1, 8, 1, 1, 8, 5, 12, 1, 1, 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, 3, 7, 7, 7, 7, 7, 3, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 24, 24, 24, 24, 24, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 14, 14, 14, 14, 14, 14, 24, 24, 24, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 319) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/319 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/319' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480825.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480825 none O=C(N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 1, 8, 1, 1, 8, 5, 12, 1, 1, 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, 3, 7, 7, 7, 7, 7, 3, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 20, 20, 20, 20, 20, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 13, 13, 13, 13, 13, 13, 13, 13, 20, 20, 20, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 320) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/320 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/320' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480825.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184480825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480825 none O=C(N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 1, 8, 1, 1, 8, 5, 12, 1, 1, 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, 3, 7, 7, 7, 7, 7, 3, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 24, 24, 24, 24, 24, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 14, 14, 14, 14, 14, 14, 24, 24, 24, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 321) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/321 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/321' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480825.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184480825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480825 none O=C(N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 1, 8, 1, 1, 8, 5, 12, 1, 1, 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, 3, 7, 7, 7, 7, 7, 3, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 20, 20, 20, 20, 20, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 13, 13, 13, 13, 13, 13, 13, 13, 20, 20, 20, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184480825 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825 Building ZINC001184480825 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184480825 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 318) grep: /scratch/xiaobo/418326/xbt-8058088.46/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(N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480825.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480825 none O=C(N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 1, 8, 1, 1, 8, 5, 12, 1, 1, 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, 3, 7, 7, 7, 7, 7, 3, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 24, 24, 24, 24, 24, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 14, 14, 14, 14, 14, 14, 24, 24, 24, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 319) grep: /scratch/xiaobo/418326/xbt-8058088.46/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(N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480825.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480825 none O=C(N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 1, 8, 1, 1, 8, 5, 12, 1, 1, 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, 3, 7, 7, 7, 7, 7, 3, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 20, 20, 20, 20, 20, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 13, 13, 13, 13, 13, 13, 13, 13, 20, 20, 20, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 320) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/320: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480825.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184480825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480825 none O=C(N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 1, 8, 1, 1, 8, 5, 12, 1, 1, 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, 3, 7, 7, 7, 7, 7, 3, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 24, 24, 24, 24, 24, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 14, 14, 14, 14, 14, 14, 24, 24, 24, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 321) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/321: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480825.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184480825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480825 none O=C(N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 1, 8, 1, 1, 8, 5, 12, 1, 1, 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, 3, 7, 7, 7, 7, 7, 3, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 20, 20, 20, 20, 20, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 13, 13, 13, 13, 13, 13, 13, 13, 20, 20, 20, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184480825 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825 Building ZINC001184480825 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184480825 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 318) grep: /scratch/xiaobo/418326/xbt-8058088.46/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(N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480825.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480825 none O=C(N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 1, 8, 1, 1, 8, 5, 12, 1, 1, 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, 3, 7, 7, 7, 7, 7, 3, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 24, 24, 24, 24, 24, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 14, 14, 14, 14, 14, 14, 24, 24, 24, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 319) grep: /scratch/xiaobo/418326/xbt-8058088.46/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(N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480825.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480825 none O=C(N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 1, 8, 1, 1, 8, 5, 12, 1, 1, 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, 3, 7, 7, 7, 7, 7, 3, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 20, 20, 20, 20, 20, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 13, 13, 13, 13, 13, 13, 13, 13, 20, 20, 20, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 320) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/320: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480825.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184480825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480825 none O=C(N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 1, 8, 1, 1, 8, 5, 12, 1, 1, 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, 3, 7, 7, 7, 7, 7, 3, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 24, 24, 24, 24, 24, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 14, 14, 14, 14, 14, 14, 24, 24, 24, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 321) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/321: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480825.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184480825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480825 none O=C(N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 1, 8, 1, 1, 8, 5, 12, 1, 1, 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, 3, 7, 7, 7, 7, 7, 3, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 20, 20, 20, 20, 20, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 13, 13, 13, 13, 13, 13, 13, 13, 20, 20, 20, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184480825 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825 Building ZINC001184480825 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184480825 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 318) grep: /scratch/xiaobo/418326/xbt-8058088.46/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(N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480825.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480825 none O=C(N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 1, 8, 1, 1, 8, 5, 12, 1, 1, 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, 3, 7, 7, 7, 7, 7, 3, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 24, 24, 24, 24, 24, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 14, 14, 14, 14, 14, 14, 24, 24, 24, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 319) grep: /scratch/xiaobo/418326/xbt-8058088.46/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(N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480825.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480825 none O=C(N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 1, 8, 1, 1, 8, 5, 12, 1, 1, 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, 3, 7, 7, 7, 7, 7, 3, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 20, 20, 20, 20, 20, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 13, 13, 13, 13, 13, 13, 13, 13, 20, 20, 20, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 320) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/320: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480825.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184480825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480825 none O=C(N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 1, 8, 1, 1, 8, 5, 12, 1, 1, 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, 3, 7, 7, 7, 7, 7, 3, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 24, 24, 24, 24, 24, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 14, 14, 14, 14, 14, 14, 24, 24, 24, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 321) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/321: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480825.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184480825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480825 none O=C(N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 1, 8, 1, 1, 8, 5, 12, 1, 1, 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, 3, 7, 7, 7, 7, 7, 3, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 20, 20, 20, 20, 20, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 13, 13, 13, 13, 13, 13, 13, 13, 20, 20, 20, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184480825 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480825 Building ZINC001184480853 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480853' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480853 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480853 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480853/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480853 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 322) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/322 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/322' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cnc2n1CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2)c1ccno1) `ZINC001184480853.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480853/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184480853 none O=C(NCc1cnc2n1CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2)c1ccno1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 1, 1, 1, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 32, 36, 36, 36, 36, 32, 17, 17, 3, 3, 3, 3, 3, 4, 4, 4, 4, 3, 3, 36, 36] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480853 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480853/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480853 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 323) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/323 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/323' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cnc2n1CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2)c1ccno1) `ZINC001184480853.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480853/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184480853 none O=C(NCc1cnc2n1CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2)c1ccno1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 1, 1, 1, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 32, 37, 37, 37, 37, 32, 17, 17, 3, 3, 3, 3, 3, 4, 4, 4, 4, 3, 3, 37, 37] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480853 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184480853 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480853/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480853/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480853 Building ZINC001184480853 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480853' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480853 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480853 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480853/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480853 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 322) grep: /scratch/xiaobo/418326/xbt-8058088.46/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(NCc1cnc2n1CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2)c1ccno1) `ZINC001184480853.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480853/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184480853 none O=C(NCc1cnc2n1CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2)c1ccno1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 1, 1, 1, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 32, 36, 36, 36, 36, 32, 17, 17, 3, 3, 3, 3, 3, 4, 4, 4, 4, 3, 3, 36, 36] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480853 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480853/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480853 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 323) grep: /scratch/xiaobo/418326/xbt-8058088.46/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(NCc1cnc2n1CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2)c1ccno1) `ZINC001184480853.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480853/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184480853 none O=C(NCc1cnc2n1CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2)c1ccno1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 1, 1, 1, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 32, 37, 37, 37, 37, 32, 17, 17, 3, 3, 3, 3, 3, 4, 4, 4, 4, 3, 3, 37, 37] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480853 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184480853 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480853/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480853/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480853 Building ZINC001184480872 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184480872 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 324) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/324 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/324' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480872.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480872 none O=C(N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 12, 1, 1, 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, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 18, 18, 15, 18, 18, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 18, 15, 18, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 325) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/325 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/325' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480872.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480872 none O=C(N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 12, 1, 1, 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, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 18, 18, 15, 18, 18, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 18, 15, 18, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 326) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/326 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/326' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480872.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184480872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480872 none O=C(N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 12, 1, 1, 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, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 18, 18, 14, 18, 18, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 18, 14, 18, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 327) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/327 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/327' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480872.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184480872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480872 none O=C(N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 12, 1, 1, 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, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 18, 18, 14, 18, 18, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 18, 14, 18, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184480872 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872 Building ZINC001184480872 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184480872 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 324) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/324: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480872.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480872 none O=C(N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 12, 1, 1, 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, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 18, 18, 15, 18, 18, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 18, 15, 18, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 325) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/325: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480872.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480872 none O=C(N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 12, 1, 1, 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, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 18, 18, 15, 18, 18, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 18, 15, 18, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 326) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/326: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480872.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184480872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480872 none O=C(N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 12, 1, 1, 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, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 18, 18, 14, 18, 18, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 18, 14, 18, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 327) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/327: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480872.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184480872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480872 none O=C(N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 12, 1, 1, 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, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 18, 18, 14, 18, 18, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 18, 14, 18, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184480872 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872 Building ZINC001184480872 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184480872 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 324) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/324: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480872.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480872 none O=C(N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 12, 1, 1, 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, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 18, 18, 15, 18, 18, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 18, 15, 18, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 325) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/325: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480872.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480872 none O=C(N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 12, 1, 1, 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, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 18, 18, 15, 18, 18, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 18, 15, 18, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 326) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/326: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480872.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184480872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480872 none O=C(N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 12, 1, 1, 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, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 18, 18, 14, 18, 18, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 18, 14, 18, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 327) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/327: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480872.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184480872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480872 none O=C(N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 12, 1, 1, 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, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 18, 18, 14, 18, 18, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 18, 14, 18, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184480872 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872 Building ZINC001184480872 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184480872 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 324) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/324: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480872.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480872 none O=C(N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 12, 1, 1, 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, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 18, 18, 15, 18, 18, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 18, 15, 18, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 325) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/325: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480872.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480872 none O=C(N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 12, 1, 1, 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, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 18, 18, 15, 18, 18, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 18, 15, 18, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 326) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/326: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480872.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184480872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480872 none O=C(N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 12, 1, 1, 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, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 18, 18, 14, 18, 18, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 18, 14, 18, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 327) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/327: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480872.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184480872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480872 none O=C(N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 12, 1, 1, 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, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 18, 18, 14, 18, 18, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 18, 14, 18, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184480872 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480872 Building ZINC001184480909 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480909' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480909 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480909 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480909/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480909 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 328) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/328 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/328' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCn2c(=O)cc(Cn3ccnc3)nc2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480909.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001184480909 none O=C(N1CCCn2c(=O)cc(Cn3ccnc3)nc2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 8, 1, 8, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 6, 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, 2, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 20, 34, 34, 34, 34, 5, 5, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 20, 20, 34, 34, 34, 5, 5, 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]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480909 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480909/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480909 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 329) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/329 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/329' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCn2c(=O)cc(Cn3ccnc3)nc2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480909.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480909/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001184480909 none O=C(N1CCCn2c(=O)cc(Cn3ccnc3)nc2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 8, 1, 8, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 6, 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, 2, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 21, 36, 36, 36, 36, 5, 5, 5, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 21, 21, 36, 36, 36, 5, 5, 3, 3, 3, 3] 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]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480909 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184480909 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480909/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480909/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480909 Building ZINC001184480909 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480909' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480909 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480909 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480909/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480909 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 328) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: O=C(N1CCCn2c(=O)cc(Cn3ccnc3)nc2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480909.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001184480909 none O=C(N1CCCn2c(=O)cc(Cn3ccnc3)nc2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 8, 1, 8, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 6, 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, 2, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 20, 34, 34, 34, 34, 5, 5, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 20, 20, 34, 34, 34, 5, 5, 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]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480909 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480909/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480909 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 329) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: O=C(N1CCCn2c(=O)cc(Cn3ccnc3)nc2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480909.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480909/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001184480909 none O=C(N1CCCn2c(=O)cc(Cn3ccnc3)nc2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 8, 1, 8, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 6, 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, 2, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 21, 36, 36, 36, 36, 5, 5, 5, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 21, 21, 36, 36, 36, 5, 5, 3, 3, 3, 3] 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]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480909 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184480909 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480909/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480909/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480909 Building ZINC001184480910 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480910' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480910 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480910 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480910/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480910 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 330) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/330 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/330' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@]1(C)C[C@H](N2CCOCC2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480910.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184480910 none COC(=O)[C@@]1(C)C[C@H](N2CCOCC2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 7, 10, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 21, 11, 11, 11, 11, 11, 11, 24, 24, 24, 24, 24, 11, 11, 8, 2, 10, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 11, 11, 11, 11, 11, 24, 24, 24, 24, 24, 24, 24, 24, 11, 11, 11, 11, 6, 6, 6, 6] 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, 56]) total number of confs: 81 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480910 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480910/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480910 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 331) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/331 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/331' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@]1(C)C[C@H](N2CCOCC2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480910.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480910/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184480910 none COC(=O)[C@@]1(C)C[C@H](N2CCOCC2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 7, 10, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 4, 11, 4, 4, 4, 4, 4, 4, 13, 13, 13, 13, 12, 4, 4, 4, 2, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 4, 4, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 4, 4, 4, 4, 6, 6, 6, 6] 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, 56]) total number of confs: 56 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480910 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184480910 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480910/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480910/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480910 Building ZINC001184480910 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480910' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480910 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480910 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480910/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480910 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 330) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COC(=O)[C@@]1(C)C[C@H](N2CCOCC2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480910.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184480910 none COC(=O)[C@@]1(C)C[C@H](N2CCOCC2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 7, 10, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 21, 11, 11, 11, 11, 11, 11, 24, 24, 24, 24, 24, 11, 11, 8, 2, 10, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 11, 11, 11, 11, 11, 24, 24, 24, 24, 24, 24, 24, 24, 11, 11, 11, 11, 6, 6, 6, 6] 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, 56]) total number of confs: 81 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480910 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480910/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480910 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 331) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COC(=O)[C@@]1(C)C[C@H](N2CCOCC2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480910.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480910/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184480910 none COC(=O)[C@@]1(C)C[C@H](N2CCOCC2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 7, 10, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 4, 11, 4, 4, 4, 4, 4, 4, 13, 13, 13, 13, 12, 4, 4, 4, 2, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 4, 4, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 4, 4, 4, 4, 6, 6, 6, 6] 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, 56]) total number of confs: 56 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480910 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184480910 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480910/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480910/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480910 Building ZINC001184480911 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480911' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480911 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480911 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480911/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480911 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 332) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/332 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/332' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@]1(C)C[C@@H](N2CCOCC2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480911.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184480911 none COC(=O)[C@]1(C)C[C@@H](N2CCOCC2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 7, 10, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 4, 11, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 11, 4, 4, 4, 2, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 4, 4, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 4, 6, 6, 6, 6] 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, 56]) total number of confs: 55 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480911 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480911/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480911 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 333) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/333 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/333' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@]1(C)C[C@@H](N2CCOCC2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480911.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480911/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184480911 none COC(=O)[C@]1(C)C[C@@H](N2CCOCC2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 7, 10, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 9, 19, 9, 9, 9, 9, 9, 9, 26, 26, 26, 26, 26, 9, 9, 8, 3, 8, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 9, 9, 9, 9, 9, 26, 26, 26, 26, 26, 26, 26, 26, 9, 9, 9, 9, 6, 6, 6, 6] 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, 56]) total number of confs: 73 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480911 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184480911 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480911/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480911/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480911 Building ZINC001184480911 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480911' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480911 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480911 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480911/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480911 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 332) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/332: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@]1(C)C[C@@H](N2CCOCC2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480911.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184480911 none COC(=O)[C@]1(C)C[C@@H](N2CCOCC2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 7, 10, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 4, 11, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 11, 4, 4, 4, 2, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 4, 4, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 4, 6, 6, 6, 6] 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, 56]) total number of confs: 55 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480911 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480911/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480911 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 333) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/333: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@]1(C)C[C@@H](N2CCOCC2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480911.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480911/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184480911 none COC(=O)[C@]1(C)C[C@@H](N2CCOCC2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 7, 10, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 9, 19, 9, 9, 9, 9, 9, 9, 26, 26, 26, 26, 26, 9, 9, 8, 3, 8, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 9, 9, 9, 9, 9, 26, 26, 26, 26, 26, 26, 26, 26, 9, 9, 9, 9, 6, 6, 6, 6] 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, 56]) total number of confs: 73 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480911 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184480911 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480911/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480911/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480911 Building ZINC001184480912 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480912' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480912 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480912 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480912/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480912 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 334) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/334 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/334' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@]1(C)C[C@@H](N2CCOCC2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480912.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184480912 none COC(=O)[C@@]1(C)C[C@@H](N2CCOCC2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 7, 10, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 7, 15, 7, 7, 7, 7, 7, 7, 17, 17, 17, 17, 17, 7, 7, 6, 2, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 15, 7, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 7, 7, 7, 7, 6, 6, 6, 6] 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, 56]) total number of confs: 59 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480912 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480912/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480912 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 335) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/335 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/335' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@]1(C)C[C@@H](N2CCOCC2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480912.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480912/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184480912 none COC(=O)[C@@]1(C)C[C@@H](N2CCOCC2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 7, 10, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 6, 12, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 6, 6, 6, 2, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 6, 6, 5, 5, 5, 5] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 52 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480912 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184480912 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480912/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480912/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480912 Building ZINC001184480912 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480912' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480912 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480912 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480912/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480912 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 334) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COC(=O)[C@@]1(C)C[C@@H](N2CCOCC2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480912.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184480912 none COC(=O)[C@@]1(C)C[C@@H](N2CCOCC2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 7, 10, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 7, 15, 7, 7, 7, 7, 7, 7, 17, 17, 17, 17, 17, 7, 7, 6, 2, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 15, 7, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 7, 7, 7, 7, 6, 6, 6, 6] 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, 56]) total number of confs: 59 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480912 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480912/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480912 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 335) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COC(=O)[C@@]1(C)C[C@@H](N2CCOCC2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480912.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480912/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184480912 none COC(=O)[C@@]1(C)C[C@@H](N2CCOCC2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 7, 10, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 6, 12, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 6, 6, 6, 2, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 6, 6, 5, 5, 5, 5] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 52 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480912 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184480912 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480912/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480912/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480912 Building ZINC001184480913 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480913' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480913 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480913 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480913/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480913 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 336) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/336 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/336' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@]1(C)C[C@H](N2CCOCC2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480913.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184480913 none COC(=O)[C@]1(C)C[C@H](N2CCOCC2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 7, 10, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 8, 16, 8, 8, 8, 8, 8, 8, 16, 16, 16, 16, 16, 8, 8, 7, 2, 7, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 16, 16, 8, 8, 8, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 8, 8, 8, 8, 5, 5, 5, 5] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 62 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480913 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480913/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480913 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 337) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/337 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/337' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@]1(C)C[C@H](N2CCOCC2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480913.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480913/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184480913 none COC(=O)[C@]1(C)C[C@H](N2CCOCC2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 7, 10, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 8, 16, 8, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 8, 8, 8, 2, 8, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 16, 16, 16, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 8, 6, 6, 6, 6] 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, 56]) total number of confs: 59 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480913 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184480913 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480913/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480913/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480913 Building ZINC001184480913 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480913' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480913 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480913 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480913/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480913 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 336) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/336: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@]1(C)C[C@H](N2CCOCC2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480913.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184480913 none COC(=O)[C@]1(C)C[C@H](N2CCOCC2)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 7, 10, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 8, 16, 8, 8, 8, 8, 8, 8, 16, 16, 16, 16, 16, 8, 8, 7, 2, 7, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 16, 16, 8, 8, 8, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 8, 8, 8, 8, 5, 5, 5, 5] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 62 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480913 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480913/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480913 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 337) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/337: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@]1(C)C[C@H](N2CCOCC2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480913.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480913/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184480913 none COC(=O)[C@]1(C)C[C@H](N2CCOCC2)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 7, 10, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 8, 16, 8, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 8, 8, 8, 2, 8, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 16, 16, 16, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 8, 6, 6, 6, 6] 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, 56]) total number of confs: 59 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480913 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184480913 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480913/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480913/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480913 Building ZINC001184480933 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480933' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480933 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480933 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480933/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480933 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 338) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/338 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/338' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCn2c(Cn3cccn3)nnc2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480933.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184480933 none O=C(N1CCCn2c(Cn3cccn3)nnc2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 5, 8, 1, 1, 1, 8, 8, 8, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 6, 8, 8, 8, 8, 8, 8, 21, 28, 28, 28, 28, 8, 8, 8, 8, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 21, 21, 28, 28, 28, 8, 8, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480933 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480933/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480933 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 339) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/339 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/339' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCn2c(Cn3cccn3)nnc2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480933.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480933/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184480933 none O=C(N1CCCn2c(Cn3cccn3)nnc2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 5, 8, 1, 1, 1, 8, 8, 8, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens need 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, 9, 9, 9, 9, 9, 9, 22, 29, 29, 29, 29, 9, 9, 9, 9, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 22, 22, 29, 29, 29, 9, 9, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480933 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184480933 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480933/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480933/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480933 Building ZINC001184480933 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480933' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480933 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480933 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480933/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480933 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 338) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/338: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCn2c(Cn3cccn3)nnc2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480933.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184480933 none O=C(N1CCCn2c(Cn3cccn3)nnc2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 5, 8, 1, 1, 1, 8, 8, 8, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 6, 8, 8, 8, 8, 8, 8, 21, 28, 28, 28, 28, 8, 8, 8, 8, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 21, 21, 28, 28, 28, 8, 8, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480933 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480933/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480933 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 339) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/339: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCn2c(Cn3cccn3)nnc2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480933.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480933/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184480933 none O=C(N1CCCn2c(Cn3cccn3)nnc2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 5, 8, 1, 1, 1, 8, 8, 8, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens need 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, 9, 9, 9, 9, 9, 9, 22, 29, 29, 29, 29, 9, 9, 9, 9, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 22, 22, 29, 29, 29, 9, 9, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480933 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184480933 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480933/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480933/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480933 Building ZINC001184480976 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184480976 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 340) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/340 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/340' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](Cc2cn3c(n2)CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CC3)CC1) `ZINC001184480976.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184480976 none C[N@]1CC[N@](Cc2cn3c(n2)CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 1, 1, 8, 1, 8, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 23, 5, 5, 5, 5, 5, 5, 5, 3, 2, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 36, 36, 36, 36, 36, 36, 36, 36, 36, 23, 23, 5, 5, 5, 4, 4, 4, 4, 5, 5, 5, 5, 36, 36, 36, 36] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 341) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/341 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/341' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](Cc2cn3c(n2)CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CC3)CC1) `ZINC001184480976.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184480976 none C[N@]1CC[N@@](Cc2cn3c(n2)CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 1, 1, 8, 1, 8, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 5, 5, 5, 5, 5, 5, 5, 3, 2, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 35, 35, 35, 35, 35, 35, 35, 35, 35, 21, 21, 5, 5, 5, 4, 4, 4, 4, 5, 5, 5, 5, 35, 35, 35, 35] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 342) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/342 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/342' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](Cc2cn3c(n2)CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CC3)CC1) `ZINC001184480976.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184480976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184480976 none C[N@]1CC[N@](Cc2cn3c(n2)CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 1, 1, 8, 1, 8, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 5, 5, 5, 5, 5, 5, 5, 3, 2, 5, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 37, 37, 37, 37, 37, 37, 37, 37, 37, 24, 24, 5, 5, 5, 3, 3, 3, 3, 5, 5, 5, 5, 37, 37, 37, 37] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 343) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/343 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/343' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](Cc2cn3c(n2)CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CC3)CC1) `ZINC001184480976.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184480976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184480976 none C[N@]1CC[N@@](Cc2cn3c(n2)CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 1, 1, 8, 1, 8, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 5, 5, 5, 5, 5, 5, 5, 3, 2, 5, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 37, 37, 37, 37, 37, 37, 37, 37, 37, 24, 24, 5, 5, 5, 3, 3, 3, 3, 5, 5, 5, 5, 37, 37, 37, 37] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184480976 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976 Building ZINC001184480976 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184480976 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 340) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: C[N@]1CC[N@](Cc2cn3c(n2)CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CC3)CC1) `ZINC001184480976.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184480976 none C[N@]1CC[N@](Cc2cn3c(n2)CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 1, 1, 8, 1, 8, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 23, 5, 5, 5, 5, 5, 5, 5, 3, 2, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 36, 36, 36, 36, 36, 36, 36, 36, 36, 23, 23, 5, 5, 5, 4, 4, 4, 4, 5, 5, 5, 5, 36, 36, 36, 36] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 341) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: C[N@]1CC[N@@](Cc2cn3c(n2)CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CC3)CC1) `ZINC001184480976.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184480976 none C[N@]1CC[N@@](Cc2cn3c(n2)CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 1, 1, 8, 1, 8, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 5, 5, 5, 5, 5, 5, 5, 3, 2, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 35, 35, 35, 35, 35, 35, 35, 35, 35, 21, 21, 5, 5, 5, 4, 4, 4, 4, 5, 5, 5, 5, 35, 35, 35, 35] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 342) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/342: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](Cc2cn3c(n2)CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CC3)CC1) `ZINC001184480976.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184480976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184480976 none C[N@]1CC[N@](Cc2cn3c(n2)CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 1, 1, 8, 1, 8, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 5, 5, 5, 5, 5, 5, 5, 3, 2, 5, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 37, 37, 37, 37, 37, 37, 37, 37, 37, 24, 24, 5, 5, 5, 3, 3, 3, 3, 5, 5, 5, 5, 37, 37, 37, 37] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 343) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/343: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](Cc2cn3c(n2)CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CC3)CC1) `ZINC001184480976.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184480976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184480976 none C[N@]1CC[N@@](Cc2cn3c(n2)CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 1, 1, 8, 1, 8, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 5, 5, 5, 5, 5, 5, 5, 3, 2, 5, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 37, 37, 37, 37, 37, 37, 37, 37, 37, 24, 24, 5, 5, 5, 3, 3, 3, 3, 5, 5, 5, 5, 37, 37, 37, 37] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184480976 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976 Building ZINC001184480976 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184480976 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 340) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: C[N@]1CC[N@](Cc2cn3c(n2)CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CC3)CC1) `ZINC001184480976.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184480976 none C[N@]1CC[N@](Cc2cn3c(n2)CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 1, 1, 8, 1, 8, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 23, 5, 5, 5, 5, 5, 5, 5, 3, 2, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 36, 36, 36, 36, 36, 36, 36, 36, 36, 23, 23, 5, 5, 5, 4, 4, 4, 4, 5, 5, 5, 5, 36, 36, 36, 36] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 341) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: C[N@]1CC[N@@](Cc2cn3c(n2)CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CC3)CC1) `ZINC001184480976.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184480976 none C[N@]1CC[N@@](Cc2cn3c(n2)CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 1, 1, 8, 1, 8, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 5, 5, 5, 5, 5, 5, 5, 3, 2, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 35, 35, 35, 35, 35, 35, 35, 35, 35, 21, 21, 5, 5, 5, 4, 4, 4, 4, 5, 5, 5, 5, 35, 35, 35, 35] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 342) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/342: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](Cc2cn3c(n2)CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CC3)CC1) `ZINC001184480976.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184480976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184480976 none C[N@]1CC[N@](Cc2cn3c(n2)CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 1, 1, 8, 1, 8, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 5, 5, 5, 5, 5, 5, 5, 3, 2, 5, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 37, 37, 37, 37, 37, 37, 37, 37, 37, 24, 24, 5, 5, 5, 3, 3, 3, 3, 5, 5, 5, 5, 37, 37, 37, 37] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 343) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/343: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](Cc2cn3c(n2)CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CC3)CC1) `ZINC001184480976.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184480976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184480976 none C[N@]1CC[N@@](Cc2cn3c(n2)CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 1, 1, 8, 1, 8, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 5, 5, 5, 5, 5, 5, 5, 3, 2, 5, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 37, 37, 37, 37, 37, 37, 37, 37, 37, 24, 24, 5, 5, 5, 3, 3, 3, 3, 5, 5, 5, 5, 37, 37, 37, 37] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184480976 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976 Building ZINC001184480976 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184480976 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 340) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: C[N@]1CC[N@](Cc2cn3c(n2)CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CC3)CC1) `ZINC001184480976.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184480976 none C[N@]1CC[N@](Cc2cn3c(n2)CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 1, 1, 8, 1, 8, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 23, 5, 5, 5, 5, 5, 5, 5, 3, 2, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 36, 36, 36, 36, 36, 36, 36, 36, 36, 23, 23, 5, 5, 5, 4, 4, 4, 4, 5, 5, 5, 5, 36, 36, 36, 36] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 341) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: C[N@]1CC[N@@](Cc2cn3c(n2)CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CC3)CC1) `ZINC001184480976.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184480976 none C[N@]1CC[N@@](Cc2cn3c(n2)CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 1, 1, 8, 1, 8, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 5, 5, 5, 5, 5, 5, 5, 3, 2, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 35, 35, 35, 35, 35, 35, 35, 35, 35, 21, 21, 5, 5, 5, 4, 4, 4, 4, 5, 5, 5, 5, 35, 35, 35, 35] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 342) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/342: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](Cc2cn3c(n2)CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CC3)CC1) `ZINC001184480976.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184480976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184480976 none C[N@]1CC[N@](Cc2cn3c(n2)CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 1, 1, 8, 1, 8, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 5, 5, 5, 5, 5, 5, 5, 3, 2, 5, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 37, 37, 37, 37, 37, 37, 37, 37, 37, 24, 24, 5, 5, 5, 3, 3, 3, 3, 5, 5, 5, 5, 37, 37, 37, 37] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 343) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/343: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](Cc2cn3c(n2)CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CC3)CC1) `ZINC001184480976.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184480976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184480976 none C[N@]1CC[N@@](Cc2cn3c(n2)CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 1, 1, 8, 1, 8, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 5, 5, 5, 5, 5, 5, 5, 3, 2, 5, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 37, 37, 37, 37, 37, 37, 37, 37, 37, 24, 24, 5, 5, 5, 3, 3, 3, 3, 5, 5, 5, 5, 37, 37, 37, 37] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184480976 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184480976 Building ZINC001184481040 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481040' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481040 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481040 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481040/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481040 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 344) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/344 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/344' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([C@H]1CC[C@@H]2[C@@H](CCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)O1)N1CCCO1) `ZINC001184481040.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481040/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184481040 none O=C([C@H]1CC[C@@H]2[C@@H](CCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)O1)N1CCCO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 7, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 12, 8, 5, 5, 5, 12, 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, 9, 6, 8, 10, 11, 7, 4, 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: [22, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 22, 24, 24, 24, 24, 8, 8, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 24, 24, 24, 24, 24, 24] 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]) total number of confs: 70 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481040 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481040/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481040 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 345) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/345 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/345' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([C@H]1CC[C@@H]2[C@@H](CCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)O1)N1CCCO1) `ZINC001184481040.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481040/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184481040 none O=C([C@H]1CC[C@@H]2[C@@H](CCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)O1)N1CCCO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 7, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 12, 8, 5, 5, 5, 12, 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, 9, 6, 8, 10, 11, 7, 4, 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: [29, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 29, 31, 31, 31, 31, 11, 11, 11, 11, 11, 11, 11, 11, 4, 4, 4, 4, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481040 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184481040 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481040/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481040/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481040 Building ZINC001184481040 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481040' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481040 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481040 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481040/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481040 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 344) grep: /scratch/xiaobo/418326/xbt-8058088.46/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([C@H]1CC[C@@H]2[C@@H](CCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)O1)N1CCCO1) `ZINC001184481040.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481040/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184481040 none O=C([C@H]1CC[C@@H]2[C@@H](CCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)O1)N1CCCO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 7, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 12, 8, 5, 5, 5, 12, 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, 9, 6, 8, 10, 11, 7, 4, 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: [22, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 22, 24, 24, 24, 24, 8, 8, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 24, 24, 24, 24, 24, 24] 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]) total number of confs: 70 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481040 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481040/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481040 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 345) grep: /scratch/xiaobo/418326/xbt-8058088.46/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([C@H]1CC[C@@H]2[C@@H](CCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)O1)N1CCCO1) `ZINC001184481040.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481040/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001184481040 none O=C([C@H]1CC[C@@H]2[C@@H](CCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)O1)N1CCCO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 7, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 12, 8, 5, 5, 5, 12, 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, 9, 6, 8, 10, 11, 7, 4, 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: [29, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 29, 31, 31, 31, 31, 11, 11, 11, 11, 11, 11, 11, 11, 4, 4, 4, 4, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481040 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184481040 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481040/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481040/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481040 Building ZINC001184481093 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481093' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481093 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481093 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481093/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481093 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 346) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/346 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/346' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2COC[C@H]12)C1CCC1) `ZINC001184481093.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481093/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001184481093 none O=C(N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2COC[C@H]12)C1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', '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: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 12, 5, 5, 7, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 13, 30, 30, 30, 11, 6, 6, 4, 4, 4, 4, 6, 6, 6, 6, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481093 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481093/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481093 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 347) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/347 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/347' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2COC[C@H]12)C1CCC1) `ZINC001184481093.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481093/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001184481093 none O=C(N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2COC[C@H]12)C1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', '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: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 12, 5, 5, 7, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 13, 30, 30, 30, 10, 5, 5, 4, 4, 4, 4, 5, 5, 5, 5, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 87 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481093 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184481093 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481093/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481093/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481093 Building ZINC001184481093 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481093' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481093 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481093 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481093/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481093 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 346) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/346: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2COC[C@H]12)C1CCC1) `ZINC001184481093.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481093/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001184481093 none O=C(N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2COC[C@H]12)C1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', '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: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 12, 5, 5, 7, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 13, 30, 30, 30, 11, 6, 6, 4, 4, 4, 4, 6, 6, 6, 6, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481093 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481093/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481093 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 347) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/347: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2COC[C@H]12)C1CCC1) `ZINC001184481093.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481093/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001184481093 none O=C(N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2COC[C@H]12)C1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', '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: [11, 1, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 12, 5, 5, 7, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 13, 30, 30, 30, 10, 5, 5, 4, 4, 4, 4, 5, 5, 5, 5, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 87 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481093 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184481093 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481093/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481093/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481093 Building ZINC001184481223 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184481223 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 348) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/348 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/348' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCO[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@@H]2C1) `ZINC001184481223.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184481223 none COCCN1CCO[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 34, 29, 15, 15, 15, 15, 15, 15, 15, 15, 8, 1, 10, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15, 36, 36, 36, 34, 34, 29, 29, 15, 15, 15, 15, 15, 15, 4, 4, 4, 4, 15, 15, 15, 15, 15, 15] 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]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 349) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/349 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/349' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCO[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@@H]2C1) `ZINC001184481223.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184481223 none COCCN1CCO[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 34, 29, 15, 15, 15, 15, 15, 15, 15, 15, 8, 1, 10, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15, 36, 36, 36, 34, 34, 29, 29, 15, 15, 15, 15, 15, 15, 4, 4, 4, 4, 15, 15, 15, 15, 15, 15] 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]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 350) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/350 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/350' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCO[C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@@H]2C1) `ZINC001184481223.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184481223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184481223 none COCCN1CCO[C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 30, 27, 16, 16, 16, 16, 16, 16, 16, 16, 9, 1, 12, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16, 16, 34, 34, 34, 30, 30, 27, 27, 16, 16, 16, 16, 16, 16, 4, 4, 4, 4, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 351) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/351 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/351' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCO[C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@@H]2C1) `ZINC001184481223.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184481223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184481223 none COCCN1CCO[C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 30, 27, 16, 16, 16, 16, 16, 16, 16, 16, 9, 1, 12, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16, 16, 34, 34, 34, 30, 30, 27, 27, 16, 16, 16, 16, 16, 16, 4, 4, 4, 4, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184481223 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223 Building ZINC001184481223 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184481223 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 348) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COCCN1CCO[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@@H]2C1) `ZINC001184481223.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184481223 none COCCN1CCO[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 34, 29, 15, 15, 15, 15, 15, 15, 15, 15, 8, 1, 10, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15, 36, 36, 36, 34, 34, 29, 29, 15, 15, 15, 15, 15, 15, 4, 4, 4, 4, 15, 15, 15, 15, 15, 15] 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]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 349) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COCCN1CCO[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@@H]2C1) `ZINC001184481223.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184481223 none COCCN1CCO[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 34, 29, 15, 15, 15, 15, 15, 15, 15, 15, 8, 1, 10, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15, 36, 36, 36, 34, 34, 29, 29, 15, 15, 15, 15, 15, 15, 4, 4, 4, 4, 15, 15, 15, 15, 15, 15] 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]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 350) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/350: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCO[C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@@H]2C1) `ZINC001184481223.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184481223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184481223 none COCCN1CCO[C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 30, 27, 16, 16, 16, 16, 16, 16, 16, 16, 9, 1, 12, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16, 16, 34, 34, 34, 30, 30, 27, 27, 16, 16, 16, 16, 16, 16, 4, 4, 4, 4, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 351) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/351: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCO[C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@@H]2C1) `ZINC001184481223.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184481223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184481223 none COCCN1CCO[C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 30, 27, 16, 16, 16, 16, 16, 16, 16, 16, 9, 1, 12, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16, 16, 34, 34, 34, 30, 30, 27, 27, 16, 16, 16, 16, 16, 16, 4, 4, 4, 4, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184481223 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223 Building ZINC001184481223 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184481223 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 348) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COCCN1CCO[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@@H]2C1) `ZINC001184481223.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184481223 none COCCN1CCO[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 34, 29, 15, 15, 15, 15, 15, 15, 15, 15, 8, 1, 10, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15, 36, 36, 36, 34, 34, 29, 29, 15, 15, 15, 15, 15, 15, 4, 4, 4, 4, 15, 15, 15, 15, 15, 15] 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]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 349) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COCCN1CCO[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@@H]2C1) `ZINC001184481223.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184481223 none COCCN1CCO[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 34, 29, 15, 15, 15, 15, 15, 15, 15, 15, 8, 1, 10, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15, 36, 36, 36, 34, 34, 29, 29, 15, 15, 15, 15, 15, 15, 4, 4, 4, 4, 15, 15, 15, 15, 15, 15] 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]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 350) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/350: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCO[C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@@H]2C1) `ZINC001184481223.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184481223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184481223 none COCCN1CCO[C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 30, 27, 16, 16, 16, 16, 16, 16, 16, 16, 9, 1, 12, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16, 16, 34, 34, 34, 30, 30, 27, 27, 16, 16, 16, 16, 16, 16, 4, 4, 4, 4, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 351) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/351: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCO[C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@@H]2C1) `ZINC001184481223.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184481223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184481223 none COCCN1CCO[C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 30, 27, 16, 16, 16, 16, 16, 16, 16, 16, 9, 1, 12, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16, 16, 34, 34, 34, 30, 30, 27, 27, 16, 16, 16, 16, 16, 16, 4, 4, 4, 4, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184481223 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223 Building ZINC001184481223 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184481223 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 348) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COCCN1CCO[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@@H]2C1) `ZINC001184481223.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184481223 none COCCN1CCO[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 34, 29, 15, 15, 15, 15, 15, 15, 15, 15, 8, 1, 10, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15, 36, 36, 36, 34, 34, 29, 29, 15, 15, 15, 15, 15, 15, 4, 4, 4, 4, 15, 15, 15, 15, 15, 15] 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]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 349) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COCCN1CCO[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@@H]2C1) `ZINC001184481223.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184481223 none COCCN1CCO[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 34, 29, 15, 15, 15, 15, 15, 15, 15, 15, 8, 1, 10, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15, 36, 36, 36, 34, 34, 29, 29, 15, 15, 15, 15, 15, 15, 4, 4, 4, 4, 15, 15, 15, 15, 15, 15] 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]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 350) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/350: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCO[C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@@H]2C1) `ZINC001184481223.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184481223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184481223 none COCCN1CCO[C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 30, 27, 16, 16, 16, 16, 16, 16, 16, 16, 9, 1, 12, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16, 16, 34, 34, 34, 30, 30, 27, 27, 16, 16, 16, 16, 16, 16, 4, 4, 4, 4, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 351) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/351: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCO[C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@@H]2C1) `ZINC001184481223.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184481223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184481223 none COCCN1CCO[C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 30, 27, 16, 16, 16, 16, 16, 16, 16, 16, 9, 1, 12, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16, 16, 34, 34, 34, 30, 30, 27, 27, 16, 16, 16, 16, 16, 16, 4, 4, 4, 4, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184481223 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481223 Building ZINC001184481277 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481277' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481277 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481277 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481277/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481277 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 352) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/352 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/352' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N1CCO[C@@]2(C1)COCCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184481277.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184481277 none CC(C)C(=O)N1CCO[C@@]2(C1)COCCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 12, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 29, 19, 27, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 13, 1, 15, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 19, 29, 29, 29, 29, 29, 29, 29, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 5, 5, 5, 5, 19, 19] 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: 86 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481277 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481277/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481277 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 353) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/353 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/353' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N1CCO[C@@]2(C1)COCCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184481277.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481277/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184481277 none CC(C)C(=O)N1CCO[C@@]2(C1)COCCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 12, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 21, 22, 14, 21, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 1, 8, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 22, 22, 22, 22, 22, 22, 22, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 5, 5, 5, 14, 14] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 63 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481277 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184481277 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481277/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481277/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481277 Building ZINC001184481277 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481277' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481277 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481277 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481277/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481277 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 352) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC(C)C(=O)N1CCO[C@@]2(C1)COCCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184481277.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184481277 none CC(C)C(=O)N1CCO[C@@]2(C1)COCCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 12, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 29, 19, 27, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 13, 1, 15, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 19, 29, 29, 29, 29, 29, 29, 29, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 5, 5, 5, 5, 19, 19] 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: 86 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481277 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481277/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481277 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 353) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC(C)C(=O)N1CCO[C@@]2(C1)COCCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184481277.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481277/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184481277 none CC(C)C(=O)N1CCO[C@@]2(C1)COCCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 12, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 21, 22, 14, 21, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 1, 8, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 22, 22, 22, 22, 22, 22, 22, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 5, 5, 5, 14, 14] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 63 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481277 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184481277 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481277/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481277/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481277 Building ZINC001184481278 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481278' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481278 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481278 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481278/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481278 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 354) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/354 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/354' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N1CCO[C@]2(C1)COCCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184481278.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184481278 none CC(C)C(=O)N1CCO[C@]2(C1)COCCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 12, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 26, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 10, 2, 11, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 17, 26, 26, 26, 26, 26, 26, 26, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5, 5, 5, 17, 17] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 73 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481278 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481278/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481278 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 355) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/355 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/355' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N1CCO[C@]2(C1)COCCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184481278.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481278/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184481278 none CC(C)C(=O)N1CCO[C@]2(C1)COCCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 12, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 22, 23, 15, 22, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 10, 2, 11, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 15, 23, 23, 23, 23, 23, 23, 23, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 6, 15, 15] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 72 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481278 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184481278 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481278/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481278/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481278 Building ZINC001184481278 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481278' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481278 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481278 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481278/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481278 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 354) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC(C)C(=O)N1CCO[C@]2(C1)COCCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184481278.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184481278 none CC(C)C(=O)N1CCO[C@]2(C1)COCCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 12, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 26, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 10, 2, 11, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 17, 26, 26, 26, 26, 26, 26, 26, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5, 5, 5, 17, 17] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 73 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481278 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481278/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481278 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 355) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC(C)C(=O)N1CCO[C@]2(C1)COCCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184481278.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481278/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184481278 none CC(C)C(=O)N1CCO[C@]2(C1)COCCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 12, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 22, 23, 15, 22, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 10, 2, 11, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 15, 23, 23, 23, 23, 23, 23, 23, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 6, 15, 15] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 72 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481278 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184481278 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481278/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481278/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481278 Building ZINC001184481286 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481286' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481286 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481286 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481286/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481286 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 356) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/356 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/356' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)Cc1nnc2n1CCCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184481286.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184481286 none CC(=O)N(C)Cc1nnc2n1CCCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 8, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 21, 25, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 25, 25, 25, 25, 25, 25, 21, 21, 7, 7, 7, 7, 7, 7, 4, 4, 4, 4, 7, 7] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481286 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481286/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481286 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 357) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/357 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/357' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)Cc1nnc2n1CCCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184481286.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481286/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184481286 none CC(=O)N(C)Cc1nnc2n1CCCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 8, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 22, 26, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 26, 26, 26, 26, 26, 26, 22, 22, 6, 6, 6, 6, 6, 6, 4, 4, 4, 4, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481286 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184481286 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481286/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481286/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481286 Building ZINC001184481286 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481286' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481286 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481286 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481286/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481286 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 356) grep: /scratch/xiaobo/418326/xbt-8058088.46/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)N(C)Cc1nnc2n1CCCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184481286.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184481286 none CC(=O)N(C)Cc1nnc2n1CCCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 8, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 21, 25, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 25, 25, 25, 25, 25, 25, 21, 21, 7, 7, 7, 7, 7, 7, 4, 4, 4, 4, 7, 7] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481286 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481286/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481286 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 357) grep: /scratch/xiaobo/418326/xbt-8058088.46/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)N(C)Cc1nnc2n1CCCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184481286.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481286/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184481286 none CC(=O)N(C)Cc1nnc2n1CCCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 8, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 22, 26, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 26, 26, 26, 26, 26, 26, 22, 22, 6, 6, 6, 6, 6, 6, 4, 4, 4, 4, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481286 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184481286 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481286/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481286/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481286 Building ZINC001184481305 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481305' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481305 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481305 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481305/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481305 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 358) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/358 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/358' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCn2nnc(Cn3ccnc3)c2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481305.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184481305 none O=C(N1CCCn2nnc(Cn3ccnc3)c2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 8, 8, 1, 5, 8, 1, 1, 8, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 18, 18, 18, 18, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 18, 18, 18, 4, 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, 42, 43, 44, 45, 46, 47]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481305 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481305/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481305 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 359) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/359 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/359' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCn2nnc(Cn3ccnc3)c2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481305.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481305/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184481305 none O=C(N1CCCn2nnc(Cn3ccnc3)c2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 8, 8, 1, 5, 8, 1, 1, 8, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 17, 32, 32, 32, 32, 6, 6, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 17, 17, 32, 32, 32, 6, 6, 3, 3, 3, 3] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481305 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184481305 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481305/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481305/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481305 Building ZINC001184481305 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481305' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481305 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481305 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481305/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481305 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 358) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/358: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCn2nnc(Cn3ccnc3)c2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481305.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184481305 none O=C(N1CCCn2nnc(Cn3ccnc3)c2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 8, 8, 1, 5, 8, 1, 1, 8, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 18, 18, 18, 18, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 18, 18, 18, 4, 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, 42, 43, 44, 45, 46, 47]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481305 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481305/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481305 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 359) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/359: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCn2nnc(Cn3ccnc3)c2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481305.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481305/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184481305 none O=C(N1CCCn2nnc(Cn3ccnc3)c2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 8, 8, 1, 5, 8, 1, 1, 8, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 17, 32, 32, 32, 32, 6, 6, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 17, 17, 32, 32, 32, 6, 6, 3, 3, 3, 3] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481305 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184481305 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481305/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481305/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481305 Building ZINC001184481425 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481425' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481425 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481425 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481425/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481425 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 360) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/360 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/360' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)[C@@H]1CCO[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@@H]21) `ZINC001184481425.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481425/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184481425 none CN(C)C(=O)[C@@H]1CCO[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 7, 5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 19, 24, 19, 19, 19, 19, 19, 19, 19, 19, 19, 12, 2, 11, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 19, 19, 19, 24, 24, 24, 24, 24, 24, 19, 19, 19, 19, 19, 19, 19, 19, 9, 9, 9, 9, 19, 19] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 66 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481425 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481425/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481425 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 361) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/361 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/361' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)[C@@H]1CCO[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@@H]21) `ZINC001184481425.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481425/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184481425 none CN(C)C(=O)[C@@H]1CCO[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 7, 5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 25, 16, 24, 16, 16, 16, 16, 16, 16, 16, 16, 16, 7, 2, 8, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 16, 16, 16, 25, 25, 25, 25, 25, 25, 16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 6, 16, 16] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 68 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481425 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184481425 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481425/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481425/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481425 Building ZINC001184481425 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481425' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481425 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481425 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481425/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481425 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 360) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/360: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)[C@@H]1CCO[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@@H]21) `ZINC001184481425.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481425/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184481425 none CN(C)C(=O)[C@@H]1CCO[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 7, 5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 19, 24, 19, 19, 19, 19, 19, 19, 19, 19, 19, 12, 2, 11, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 19, 19, 19, 24, 24, 24, 24, 24, 24, 19, 19, 19, 19, 19, 19, 19, 19, 9, 9, 9, 9, 19, 19] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 66 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481425 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481425/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481425 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 361) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/361: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)[C@@H]1CCO[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@@H]21) `ZINC001184481425.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481425/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184481425 none CN(C)C(=O)[C@@H]1CCO[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 7, 5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 25, 16, 24, 16, 16, 16, 16, 16, 16, 16, 16, 16, 7, 2, 8, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 16, 16, 16, 25, 25, 25, 25, 25, 25, 16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 6, 16, 16] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 68 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481425 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184481425 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481425/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481425/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184481425 Building ZINC001184484322 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184484322' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184484322 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484322 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184484322/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184484322 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 362) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/362 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/362' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)NCC(=O)OCc1ccccc1) `ZINC001184484322.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184484322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184484322 none O=C(CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)NCC(=O)OCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', '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'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 8, 5, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 16, 16, 16, 17, 32, 34, 34, 33, 34, 34, 6, 6, 3, 6, 6, 6, 6, 11, 16, 16, 32, 32, 34, 34, 34, 34, 34] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184484322 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184484322/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184484322 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 363) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/363 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/363' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)NCC(=O)OCc1ccccc1) `ZINC001184484322.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184484322/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184484322 none O=C(CNC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)NCC(=O)OCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', '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'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 8, 5, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 16, 16, 16, 17, 32, 34, 34, 33, 34, 34, 6, 6, 3, 6, 6, 6, 6, 11, 16, 16, 32, 32, 34, 34, 34, 34, 34] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184484322 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184484322 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184484322/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184484322/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184484322 Building ZINC001184484322 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184484322' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184484322 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484322 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184484322/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184484322 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 362) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/362: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)NCC(=O)OCc1ccccc1) `ZINC001184484322.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184484322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184484322 none O=C(CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)NCC(=O)OCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', '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'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 8, 5, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 16, 16, 16, 17, 32, 34, 34, 33, 34, 34, 6, 6, 3, 6, 6, 6, 6, 11, 16, 16, 32, 32, 34, 34, 34, 34, 34] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184484322 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184484322/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184484322 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 363) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/363: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)NCC(=O)OCc1ccccc1) `ZINC001184484322.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184484322/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184484322 none O=C(CNC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)NCC(=O)OCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', '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'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 8, 5, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 16, 16, 16, 17, 32, 34, 34, 33, 34, 34, 6, 6, 3, 6, 6, 6, 6, 11, 16, 16, 32, 32, 34, 34, 34, 34, 34] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184484322 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184484322 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184484322/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184484322/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184484322 Building ZINC001184485539 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485539' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485539 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485539 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485539/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485539 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 364) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/364 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/364' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1) `ZINC001184485539.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184485539 none CC(C)(C)OC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 24, 20, 11, 20, 11, 11, 11, 11, 11, 3, 11, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 24, 24, 24, 24, 24, 24, 24, 24, 24, 11, 11, 33, 3, 6, 6, 6, 6, 11, 11] 150 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485539 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485539/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485539 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 365) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/365 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/365' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1) `ZINC001184485539.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485539/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184485539 none CC(C)(C)OC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 22, 17, 9, 17, 9, 9, 9, 9, 9, 4, 9, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 9, 9, 27, 3, 7, 7, 7, 7, 9, 9] 150 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485539 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184485539 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485539/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485539/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485539 Building ZINC001184485539 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485539' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485539 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485539 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485539/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485539 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 364) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/364: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1) `ZINC001184485539.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184485539 none CC(C)(C)OC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 24, 20, 11, 20, 11, 11, 11, 11, 11, 3, 11, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 24, 24, 24, 24, 24, 24, 24, 24, 24, 11, 11, 33, 3, 6, 6, 6, 6, 11, 11] 150 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485539 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485539/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485539 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 365) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/365: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1) `ZINC001184485539.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485539/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001184485539 none CC(C)(C)OC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 22, 17, 9, 17, 9, 9, 9, 9, 9, 4, 9, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 9, 9, 27, 3, 7, 7, 7, 7, 9, 9] 150 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485539 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184485539 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485539/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485539/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485539 Building ZINC001184485571 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485571' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485571 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485571 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485571/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485571 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 366) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/366 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/366' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)NC(=O)Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cc1) `ZINC001184485571.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001184485571 none CS(=O)(=O)NC(=O)Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.am', 'C.2', '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', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 1, 11, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 26, 12, 12, 12, 12, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 26, 26, 26, 26, 13, 13, 12, 12, 3, 5, 5, 5, 5, 12, 12] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485571 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485571/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485571 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 367) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/367 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/367' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)NC(=O)Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cc1) `ZINC001184485571.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485571/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001184485571 none CS(=O)(=O)NC(=O)Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.am', 'C.2', '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', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 1, 11, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 27, 12, 5, 13, 13, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 27, 27, 27, 27, 13, 13, 13, 13, 3, 4, 4, 4, 4, 13, 13] 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]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485571 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184485571 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485571/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485571/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485571 Building ZINC001184485571 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485571' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485571 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485571 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485571/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485571 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 366) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CS(=O)(=O)NC(=O)Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cc1) `ZINC001184485571.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001184485571 none CS(=O)(=O)NC(=O)Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.am', 'C.2', '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', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 1, 11, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 26, 12, 12, 12, 12, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 26, 26, 26, 26, 13, 13, 12, 12, 3, 5, 5, 5, 5, 12, 12] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485571 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485571/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485571 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 367) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CS(=O)(=O)NC(=O)Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cc1) `ZINC001184485571.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485571/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001184485571 none CS(=O)(=O)NC(=O)Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.am', 'C.2', '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', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 1, 11, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 27, 12, 5, 13, 13, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 27, 27, 27, 27, 13, 13, 13, 13, 3, 4, 4, 4, 4, 13, 13] 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]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485571 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184485571 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485571/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485571/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485571 Building ZINC001184485578 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485578' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485578 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485578 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485578/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485578 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 368) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/368 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/368' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](NS(=O)(=O)c2ccccn2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485578.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184485578 none O=C(N1CC[C@@H](NS(=O)(=O)c2ccccn2)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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] 0 hydrogens need rotated 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, 5, 5, 5, 5, 5, 13, 27, 27, 27, 42, 42, 42, 42, 42, 5, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 13, 42, 42, 42, 42, 5, 5, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 18, 19, 20] set([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: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485578 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485578/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485578 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 369) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/369 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/369' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](NS(=O)(=O)c2ccccn2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485578.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485578/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184485578 none O=C(N1CC[C@@H](NS(=O)(=O)c2ccccn2)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 6, 6, 6, 6, 6, 13, 26, 26, 26, 41, 41, 41, 41, 41, 6, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 13, 41, 41, 41, 41, 6, 6, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 18, 19, 20] set([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: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485578 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184485578 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485578/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485578/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485578 Building ZINC001184485578 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485578' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485578 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485578 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485578/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485578 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 368) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: O=C(N1CC[C@@H](NS(=O)(=O)c2ccccn2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485578.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184485578 none O=C(N1CC[C@@H](NS(=O)(=O)c2ccccn2)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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] 0 hydrogens need rotated 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, 5, 5, 5, 5, 5, 13, 27, 27, 27, 42, 42, 42, 42, 42, 5, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 13, 42, 42, 42, 42, 5, 5, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 18, 19, 20] set([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: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485578 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485578/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485578 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 369) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: O=C(N1CC[C@@H](NS(=O)(=O)c2ccccn2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485578.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485578/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184485578 none O=C(N1CC[C@@H](NS(=O)(=O)c2ccccn2)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 6, 6, 6, 6, 6, 13, 26, 26, 26, 41, 41, 41, 41, 41, 6, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 13, 41, 41, 41, 41, 6, 6, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 18, 19, 20] set([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: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485578 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184485578 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485578/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485578/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485578 Building ZINC001184485579 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485579' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485579 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485579 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485579/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485579 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 370) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/370 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/370' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](NS(=O)(=O)c2ccccn2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485579.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485579/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184485579 none O=C(N1CC[C@H](NS(=O)(=O)c2ccccn2)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 3, 3, 3, 3, 3, 11, 23, 23, 23, 41, 41, 41, 41, 41, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 41, 41, 41, 41, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 18, 19, 20] set([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: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485579 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485579/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485579 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 371) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/371 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/371' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](NS(=O)(=O)c2ccccn2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485579.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485579/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184485579 none O=C(N1CC[C@H](NS(=O)(=O)c2ccccn2)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 4, 4, 4, 4, 4, 10, 19, 19, 19, 35, 35, 35, 35, 35, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 10, 35, 35, 35, 35, 4, 4, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 18, 19, 20] set([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: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485579 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184485579 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485579/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485579/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485579 Building ZINC001184485579 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485579' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485579 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485579 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485579/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485579 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 370) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/370: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](NS(=O)(=O)c2ccccn2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485579.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485579/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184485579 none O=C(N1CC[C@H](NS(=O)(=O)c2ccccn2)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 3, 3, 3, 3, 3, 11, 23, 23, 23, 41, 41, 41, 41, 41, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 41, 41, 41, 41, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 18, 19, 20] set([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: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485579 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485579/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485579 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 371) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/371: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](NS(=O)(=O)c2ccccn2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485579.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485579/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184485579 none O=C(N1CC[C@H](NS(=O)(=O)c2ccccn2)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 4, 4, 4, 4, 4, 10, 19, 19, 19, 35, 35, 35, 35, 35, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 10, 35, 35, 35, 35, 4, 4, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 18, 19, 20] set([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: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485579 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184485579 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485579/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485579/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485579 Building ZINC001184485857 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485857' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485857 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485857 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485857/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485857 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 372) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/372 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/372' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21) `ZINC001184485857.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001184485857 none CCOC(=O)[C@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 11, 9, 4, 9, 4, 4, 4, 4, 4, 12, 12, 19, 21, 21, 21, 4, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 18, 18, 18, 18, 18, 4, 4, 21, 21, 21, 21, 21, 21, 21, 21, 21, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 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/418326/xbt-8058088.46/working/building/ZINC001184485857 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485857/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485857 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 373) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/373 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/373' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21) `ZINC001184485857.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485857/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001184485857 none CCOC(=O)[C@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 13, 11, 4, 11, 4, 4, 4, 4, 4, 7, 7, 10, 10, 10, 10, 4, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 5, 17, 17, 17, 17, 17, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 4, 4, 5, 5, 5, 8, 8, 8, 5] 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: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485857 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184485857 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485857/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485857/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485857 Building ZINC001184485857 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485857' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485857 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485857 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485857/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485857 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 372) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCOC(=O)[C@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21) `ZINC001184485857.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001184485857 none CCOC(=O)[C@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 11, 9, 4, 9, 4, 4, 4, 4, 4, 12, 12, 19, 21, 21, 21, 4, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 18, 18, 18, 18, 18, 4, 4, 21, 21, 21, 21, 21, 21, 21, 21, 21, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 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/418326/xbt-8058088.46/working/building/ZINC001184485857 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485857/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485857 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 373) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCOC(=O)[C@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21) `ZINC001184485857.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485857/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001184485857 none CCOC(=O)[C@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 13, 11, 4, 11, 4, 4, 4, 4, 4, 7, 7, 10, 10, 10, 10, 4, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 5, 17, 17, 17, 17, 17, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 4, 4, 5, 5, 5, 8, 8, 8, 5] 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: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485857 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184485857 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485857/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485857/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485857 Building ZINC001184485859 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485859' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485859 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485859 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485859/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485859 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 374) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/374 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/374' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21) `ZINC001184485859.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001184485859 none CCOC(=O)[C@@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 16, 15, 6, 15, 6, 6, 6, 6, 6, 10, 10, 17, 17, 17, 17, 6, 6, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 5, 18, 18, 18, 18, 18, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 6, 6, 5, 5, 5, 8, 8, 8, 5] 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: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485859 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485859/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485859 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 375) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/375 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/375' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21) `ZINC001184485859.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485859/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001184485859 none CCOC(=O)[C@@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 5, 11, 5, 5, 5, 5, 5, 11, 11, 21, 21, 21, 21, 5, 5, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 7, 4, 4, 21, 21, 21, 21, 21, 5, 5, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 5, 5, 5, 4, 4, 4, 7, 7, 7, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485859 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184485859 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485859/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485859/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485859 Building ZINC001184485859 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485859' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485859 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485859 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485859/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485859 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 374) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCOC(=O)[C@@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21) `ZINC001184485859.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001184485859 none CCOC(=O)[C@@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 16, 15, 6, 15, 6, 6, 6, 6, 6, 10, 10, 17, 17, 17, 17, 6, 6, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 5, 18, 18, 18, 18, 18, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 6, 6, 5, 5, 5, 8, 8, 8, 5] 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: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485859 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485859/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485859 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 375) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCOC(=O)[C@@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21) `ZINC001184485859.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485859/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001184485859 none CCOC(=O)[C@@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 5, 11, 5, 5, 5, 5, 5, 11, 11, 21, 21, 21, 21, 5, 5, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 7, 4, 4, 21, 21, 21, 21, 21, 5, 5, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 5, 5, 5, 4, 4, 4, 7, 7, 7, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485859 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184485859 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485859/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485859/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184485859 Building ZINC001184486024 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486024' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486024 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486024 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486024/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486024 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 376) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/376 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/376' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4C[C@H](C(=O)NCCc5ccccn5)O[C@H]4C3)c2c1) `ZINC001184486024.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184486024 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4C[C@H](C(=O)NCCc5ccccn5)O[C@H]4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 8, 12, 5, 7, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 2, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 16, 16, 16, 31, 39, 43, 43, 43, 43, 43, 9, 9, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 9, 9, 16, 31, 31, 39, 39, 43, 43, 43, 43, 9, 9, 2] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486024 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486024/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486024 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 377) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/377 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/377' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4C[C@H](C(=O)NCCc5ccccn5)O[C@H]4C3)c2c1) `ZINC001184486024.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486024/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184486024 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4C[C@H](C(=O)NCCc5ccccn5)O[C@H]4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 8, 12, 5, 7, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 8, 9, 9, 9, 9, 9, 9, 9, 9, 12, 12, 12, 21, 27, 32, 32, 32, 32, 32, 9, 9, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 12, 21, 21, 27, 27, 32, 32, 32, 32, 9, 9, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486024 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184486024 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486024/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486024/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486024 Building ZINC001184486024 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486024' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486024 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486024 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486024/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486024 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 376) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4C[C@H](C(=O)NCCc5ccccn5)O[C@H]4C3)c2c1) `ZINC001184486024.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184486024 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4C[C@H](C(=O)NCCc5ccccn5)O[C@H]4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 8, 12, 5, 7, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 2, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 16, 16, 16, 31, 39, 43, 43, 43, 43, 43, 9, 9, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 9, 9, 16, 31, 31, 39, 39, 43, 43, 43, 43, 9, 9, 2] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486024 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486024/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486024 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 377) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4C[C@H](C(=O)NCCc5ccccn5)O[C@H]4C3)c2c1) `ZINC001184486024.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486024/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184486024 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4C[C@H](C(=O)NCCc5ccccn5)O[C@H]4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 8, 12, 5, 7, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 8, 9, 9, 9, 9, 9, 9, 9, 9, 12, 12, 12, 21, 27, 32, 32, 32, 32, 32, 9, 9, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 12, 21, 21, 27, 27, 32, 32, 32, 32, 9, 9, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486024 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184486024 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486024/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486024/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486024 Building ZINC001184486082 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486082' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486082 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486082 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486082/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486082 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 378) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/378 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/378' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCN(CCNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C(=O)C1) `ZINC001184486082.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184486082 none CC(C)(C)OC(=O)N1CCN(CCNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C(=O)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', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 25, 21, 21, 14, 10, 5, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 21, 21, 21, 25, 25, 25, 25, 25, 25, 25, 25, 25, 21, 21, 21, 21, 5, 5, 5, 5, 3, 5, 5, 5, 5, 21, 21] 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486082 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486082/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486082 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 379) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/379 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/379' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCN(CCNC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C(=O)C1) `ZINC001184486082.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486082/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184486082 none CC(C)(C)OC(=O)N1CCN(CCNC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C(=O)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', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 25, 21, 21, 14, 10, 5, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 21, 21, 21, 25, 25, 25, 25, 25, 25, 25, 25, 25, 21, 21, 21, 21, 5, 5, 5, 5, 3, 5, 5, 5, 5, 21, 21] 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486082 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184486082 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486082/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486082/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486082 Building ZINC001184486082 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486082' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486082 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486082 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486082/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486082 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 378) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/378: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCN(CCNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C(=O)C1) `ZINC001184486082.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184486082 none CC(C)(C)OC(=O)N1CCN(CCNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C(=O)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', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 25, 21, 21, 14, 10, 5, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 21, 21, 21, 25, 25, 25, 25, 25, 25, 25, 25, 25, 21, 21, 21, 21, 5, 5, 5, 5, 3, 5, 5, 5, 5, 21, 21] 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486082 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486082/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486082 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 379) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/379: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCN(CCNC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C(=O)C1) `ZINC001184486082.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486082/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184486082 none CC(C)(C)OC(=O)N1CCN(CCNC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C(=O)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', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 25, 21, 21, 14, 10, 5, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 21, 21, 21, 25, 25, 25, 25, 25, 25, 25, 25, 25, 21, 21, 21, 21, 5, 5, 5, 5, 3, 5, 5, 5, 5, 21, 21] 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486082 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184486082 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486082/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486082/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486082 Building ZINC001184486098 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486098' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486098 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486098 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486098/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486098 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 380) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/380 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/380' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCOC[C@@]4(C[C@H](CNc5ccc(C)nn5)CO4)C3)c2c1) `ZINC001184486098.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486098/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184486098 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCOC[C@@]4(C[C@H](CNc5ccc(C)nn5)CO4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'N.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 7, 5, 8, 1, 1, 1, 1, 5, 8, 8, 5, 12, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 11, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 22, 33, 38, 38, 38, 38, 38, 38, 13, 13, 13, 5, 5, 6, 6, 6, 5, 5, 5, 13, 13, 13, 13, 13, 13, 13, 13, 22, 22, 33, 38, 38, 38, 38, 38, 13, 13, 13, 13, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486098 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486098/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486098 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 381) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/381 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/381' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCOC[C@@]4(C[C@H](CNc5ccc(C)nn5)CO4)C3)c2c1) `ZINC001184486098.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486098/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184486098 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCOC[C@@]4(C[C@H](CNc5ccc(C)nn5)CO4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'N.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 7, 5, 8, 1, 1, 1, 1, 5, 8, 8, 5, 12, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 32, 34, 34, 34, 34, 34, 34, 4, 4, 4, 5, 5, 7, 7, 7, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 32, 34, 34, 34, 34, 34, 4, 4, 4, 4, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 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/418326/xbt-8058088.46/working/building/ZINC001184486098 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184486098 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486098/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486098/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486098 Building ZINC001184486098 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486098' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486098 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486098 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486098/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486098 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 380) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCOC[C@@]4(C[C@H](CNc5ccc(C)nn5)CO4)C3)c2c1) `ZINC001184486098.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486098/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184486098 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCOC[C@@]4(C[C@H](CNc5ccc(C)nn5)CO4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'N.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 7, 5, 8, 1, 1, 1, 1, 5, 8, 8, 5, 12, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 11, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 22, 33, 38, 38, 38, 38, 38, 38, 13, 13, 13, 5, 5, 6, 6, 6, 5, 5, 5, 13, 13, 13, 13, 13, 13, 13, 13, 22, 22, 33, 38, 38, 38, 38, 38, 13, 13, 13, 13, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486098 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486098/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486098 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 381) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCOC[C@@]4(C[C@H](CNc5ccc(C)nn5)CO4)C3)c2c1) `ZINC001184486098.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486098/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184486098 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCOC[C@@]4(C[C@H](CNc5ccc(C)nn5)CO4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'N.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 7, 5, 8, 1, 1, 1, 1, 5, 8, 8, 5, 12, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 32, 34, 34, 34, 34, 34, 34, 4, 4, 4, 5, 5, 7, 7, 7, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 32, 34, 34, 34, 34, 34, 4, 4, 4, 4, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 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/418326/xbt-8058088.46/working/building/ZINC001184486098 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184486098 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486098/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486098/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486098 Building ZINC001184486109 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486109' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486109 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486109 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486109/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486109 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 382) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/382 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/382' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCOC[C@]4(C[C@@H](CNc5ccc(C)nn5)CO4)C3)c2c1) `ZINC001184486109.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184486109 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCOC[C@]4(C[C@@H](CNc5ccc(C)nn5)CO4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'N.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 7, 5, 8, 1, 1, 1, 1, 5, 8, 8, 5, 12, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 33, 37, 37, 37, 37, 37, 37, 5, 5, 5, 5, 5, 6, 6, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 16, 33, 37, 37, 37, 37, 37, 5, 5, 5, 5, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486109 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486109/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486109 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 383) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/383 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/383' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCOC[C@]4(C[C@@H](CNc5ccc(C)nn5)CO4)C3)c2c1) `ZINC001184486109.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486109/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184486109 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCOC[C@]4(C[C@@H](CNc5ccc(C)nn5)CO4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'N.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 7, 5, 8, 1, 1, 1, 1, 5, 8, 8, 5, 12, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 28, 34, 34, 34, 34, 34, 34, 4, 4, 4, 4, 4, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 28, 34, 34, 34, 34, 34, 4, 4, 4, 4, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486109 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184486109 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486109/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486109/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486109 Building ZINC001184486109 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486109' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486109 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486109 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486109/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486109 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 382) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCOC[C@]4(C[C@@H](CNc5ccc(C)nn5)CO4)C3)c2c1) `ZINC001184486109.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184486109 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCOC[C@]4(C[C@@H](CNc5ccc(C)nn5)CO4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'N.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 7, 5, 8, 1, 1, 1, 1, 5, 8, 8, 5, 12, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 33, 37, 37, 37, 37, 37, 37, 5, 5, 5, 5, 5, 6, 6, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 16, 33, 37, 37, 37, 37, 37, 5, 5, 5, 5, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486109 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486109/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486109 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 383) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCOC[C@]4(C[C@@H](CNc5ccc(C)nn5)CO4)C3)c2c1) `ZINC001184486109.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486109/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184486109 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCOC[C@]4(C[C@@H](CNc5ccc(C)nn5)CO4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'N.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 7, 5, 8, 1, 1, 1, 1, 5, 8, 8, 5, 12, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 28, 34, 34, 34, 34, 34, 34, 4, 4, 4, 4, 4, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 28, 34, 34, 34, 34, 34, 4, 4, 4, 4, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486109 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184486109 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486109/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486109/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486109 Building ZINC001184486110 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486110' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486110 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486110 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486110/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486110 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 384) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/384 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/384' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCOC[C@]4(C[C@H](CNc5ccc(C)nn5)CO4)C3)c2c1) `ZINC001184486110.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184486110 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCOC[C@]4(C[C@H](CNc5ccc(C)nn5)CO4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'N.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 7, 5, 8, 1, 1, 1, 1, 5, 8, 8, 5, 12, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 2, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 13, 30, 33, 33, 33, 33, 33, 33, 5, 5, 5, 3, 3, 4, 4, 4, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 13, 13, 30, 33, 33, 33, 33, 33, 5, 5, 5, 5, 3] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486110 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486110/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486110 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 385) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/385 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/385' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCOC[C@]4(C[C@H](CNc5ccc(C)nn5)CO4)C3)c2c1) `ZINC001184486110.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486110/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184486110 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCOC[C@]4(C[C@H](CNc5ccc(C)nn5)CO4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'N.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 7, 5, 8, 1, 1, 1, 1, 5, 8, 8, 5, 12, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 24, 26, 26, 26, 26, 26, 26, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 24, 26, 26, 26, 26, 26, 4, 4, 4, 4, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486110 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184486110 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486110/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486110/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486110 Building ZINC001184486110 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486110' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486110 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486110 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486110/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486110 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 384) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCOC[C@]4(C[C@H](CNc5ccc(C)nn5)CO4)C3)c2c1) `ZINC001184486110.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184486110 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCOC[C@]4(C[C@H](CNc5ccc(C)nn5)CO4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'N.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 7, 5, 8, 1, 1, 1, 1, 5, 8, 8, 5, 12, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 2, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 13, 30, 33, 33, 33, 33, 33, 33, 5, 5, 5, 3, 3, 4, 4, 4, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 13, 13, 30, 33, 33, 33, 33, 33, 5, 5, 5, 5, 3] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486110 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486110/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486110 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 385) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCOC[C@]4(C[C@H](CNc5ccc(C)nn5)CO4)C3)c2c1) `ZINC001184486110.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486110/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184486110 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCOC[C@]4(C[C@H](CNc5ccc(C)nn5)CO4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'N.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 7, 5, 8, 1, 1, 1, 1, 5, 8, 8, 5, 12, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 24, 26, 26, 26, 26, 26, 26, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 24, 26, 26, 26, 26, 26, 4, 4, 4, 4, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486110 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184486110 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486110/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486110/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486110 Building ZINC001184486114 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486114' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486114 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486114 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486114/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486114 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 386) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/386 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/386' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCOC[C@@]4(C[C@@H](CNc5ccc(C)nn5)CO4)C3)c2c1) `ZINC001184486114.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184486114 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCOC[C@@]4(C[C@@H](CNc5ccc(C)nn5)CO4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'N.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 7, 5, 8, 1, 1, 1, 1, 5, 8, 8, 5, 12, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need 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, 4, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 20, 32, 34, 34, 34, 34, 34, 34, 9, 9, 9, 4, 4, 5, 5, 5, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 20, 20, 32, 34, 34, 34, 34, 34, 9, 9, 9, 9, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486114 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486114/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486114 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 387) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/387 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/387' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCOC[C@@]4(C[C@@H](CNc5ccc(C)nn5)CO4)C3)c2c1) `ZINC001184486114.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486114/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184486114 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCOC[C@@]4(C[C@@H](CNc5ccc(C)nn5)CO4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'N.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 7, 5, 8, 1, 1, 1, 1, 5, 8, 8, 5, 12, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need 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, 7, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 16, 33, 37, 37, 37, 37, 37, 37, 10, 10, 10, 4, 4, 5, 5, 5, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 16, 16, 33, 37, 37, 37, 37, 37, 10, 10, 10, 10, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486114 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184486114 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486114/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486114/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486114 Building ZINC001184486114 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486114' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486114 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486114 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486114/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486114 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 386) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCOC[C@@]4(C[C@@H](CNc5ccc(C)nn5)CO4)C3)c2c1) `ZINC001184486114.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184486114 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCOC[C@@]4(C[C@@H](CNc5ccc(C)nn5)CO4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'N.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 7, 5, 8, 1, 1, 1, 1, 5, 8, 8, 5, 12, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need 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, 4, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 20, 32, 34, 34, 34, 34, 34, 34, 9, 9, 9, 4, 4, 5, 5, 5, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 20, 20, 32, 34, 34, 34, 34, 34, 9, 9, 9, 9, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486114 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486114/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486114 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 387) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCOC[C@@]4(C[C@@H](CNc5ccc(C)nn5)CO4)C3)c2c1) `ZINC001184486114.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486114/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184486114 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCOC[C@@]4(C[C@@H](CNc5ccc(C)nn5)CO4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'N.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 7, 5, 8, 1, 1, 1, 1, 5, 8, 8, 5, 12, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need 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, 7, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 16, 33, 37, 37, 37, 37, 37, 37, 10, 10, 10, 4, 4, 5, 5, 5, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 16, 16, 33, 37, 37, 37, 37, 37, 10, 10, 10, 10, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486114 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184486114 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486114/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486114/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486114 Building ZINC001184486198 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486198' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486198 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486198 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486198/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486198 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 388) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/388 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/388' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cc(N2CCS(=O)(=O)CC2)ccn1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486198.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184486198 none O=C(NCc1cc(N2CCS(=O)(=O)CC2)ccn1)[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', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 5, 5, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 12, 14, 14, 20, 32, 32, 32, 32, 32, 32, 32, 14, 14, 14, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 12, 12, 14, 32, 32, 32, 32, 32, 32, 32, 32, 14, 14, 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, 47, 48]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486198 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486198/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486198 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 389) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/389 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/389' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cc(N2CCS(=O)(=O)CC2)ccn1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486198.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486198/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184486198 none O=C(NCc1cc(N2CCS(=O)(=O)CC2)ccn1)[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', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 5, 5, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 12, 14, 14, 19, 32, 32, 32, 32, 32, 32, 32, 14, 14, 14, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 12, 12, 14, 32, 32, 32, 32, 32, 32, 32, 32, 14, 14, 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, 47, 48]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486198 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184486198 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486198/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486198/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486198 Building ZINC001184486198 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486198' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486198 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486198 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486198/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486198 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 388) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: O=C(NCc1cc(N2CCS(=O)(=O)CC2)ccn1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486198.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184486198 none O=C(NCc1cc(N2CCS(=O)(=O)CC2)ccn1)[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', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 5, 5, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 12, 14, 14, 20, 32, 32, 32, 32, 32, 32, 32, 14, 14, 14, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 12, 12, 14, 32, 32, 32, 32, 32, 32, 32, 32, 14, 14, 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, 47, 48]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486198 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486198/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486198 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 389) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: O=C(NCc1cc(N2CCS(=O)(=O)CC2)ccn1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486198.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486198/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184486198 none O=C(NCc1cc(N2CCS(=O)(=O)CC2)ccn1)[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', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 5, 5, 14, 11, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 12, 14, 14, 19, 32, 32, 32, 32, 32, 32, 32, 14, 14, 14, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 12, 12, 14, 32, 32, 32, 32, 32, 32, 32, 32, 14, 14, 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, 47, 48]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486198 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184486198 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486198/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486198/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486198 Building ZINC001184486496 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486496' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486496 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486496 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486496/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486496 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 390) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/390 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/390' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ncc(I)cc3C(N)=O)c2c1) `ZINC001184486496.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001184486496 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ncc(I)cc3C(N)=O)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 18, 1, 1, 1, 8, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 20, 20, 7, 7, 11, 11, 11, 7, 7, 7, 3, 14, 14, 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]) total number of confs: 60 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486496 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486496/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486496 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 391) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/391 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/391' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ncc(I)cc3C(N)=O)c2c1) `ZINC001184486496.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486496/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001184486496 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ncc(I)cc3C(N)=O)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 18, 1, 1, 1, 8, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 20, 20, 7, 7, 11, 11, 11, 7, 7, 7, 3, 14, 14, 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]) total number of confs: 60 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486496 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184486496 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486496/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486496/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486496 Building ZINC001184486496 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486496' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486496 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486496 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486496/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486496 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 390) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ncc(I)cc3C(N)=O)c2c1) `ZINC001184486496.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001184486496 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ncc(I)cc3C(N)=O)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 18, 1, 1, 1, 8, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 20, 20, 7, 7, 11, 11, 11, 7, 7, 7, 3, 14, 14, 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]) total number of confs: 60 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486496 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486496/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486496 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 391) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ncc(I)cc3C(N)=O)c2c1) `ZINC001184486496.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486496/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001184486496 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ncc(I)cc3C(N)=O)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 18, 1, 1, 1, 8, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 20, 20, 7, 7, 11, 11, 11, 7, 7, 7, 3, 14, 14, 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]) total number of confs: 60 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486496 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184486496 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486496/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486496/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486496 Building ZINC001184486722 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486722' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486722 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486722 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486722/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486722 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 392) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/392 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/392' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)C(=O)N[C@@H](C)C(=O)OC(C)(C)C) `ZINC001184486722.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184486722 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)C(=O)N[C@@H](C)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 11, 8, 5, 7, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 6, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 11, 11, 11, 17, 17, 17, 31, 31, 36, 36, 36, 36, 6, 6, 6, 3, 5, 5, 5, 5, 11, 17, 17, 17, 36, 36, 36, 36, 36, 36, 36, 36, 36] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486722 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486722/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486722 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 393) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/393 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/393' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)C(=O)N[C@@H](C)C(=O)OC(C)(C)C) `ZINC001184486722.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486722/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184486722 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)C(=O)N[C@@H](C)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 11, 8, 5, 7, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 19, 19, 19, 23, 23, 28, 28, 28, 28, 6, 6, 6, 4, 6, 6, 6, 6, 9, 19, 19, 19, 28, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 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/418326/xbt-8058088.46/working/building/ZINC001184486722 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184486722 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486722/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486722/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486722 Building ZINC001184486722 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486722' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486722 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486722 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486722/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486722 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 392) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/392: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)C(=O)N[C@@H](C)C(=O)OC(C)(C)C) `ZINC001184486722.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184486722 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)C(=O)N[C@@H](C)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 11, 8, 5, 7, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 6, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 11, 11, 11, 17, 17, 17, 31, 31, 36, 36, 36, 36, 6, 6, 6, 3, 5, 5, 5, 5, 11, 17, 17, 17, 36, 36, 36, 36, 36, 36, 36, 36, 36] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486722 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486722/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486722 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 393) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/393: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)C(=O)N[C@@H](C)C(=O)OC(C)(C)C) `ZINC001184486722.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486722/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184486722 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)C(=O)N[C@@H](C)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 11, 8, 5, 7, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 19, 19, 19, 23, 23, 28, 28, 28, 28, 6, 6, 6, 4, 6, 6, 6, 6, 9, 19, 19, 19, 28, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 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/418326/xbt-8058088.46/working/building/ZINC001184486722 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184486722 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486722/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486722/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486722 Building ZINC001184486777 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486777' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486777 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486777 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486777/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486777 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 394) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/394 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/394' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCN(S(=O)(=O)c2ccccn2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486777.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184486777 none O=C(NC1CCN(S(=O)(=O)c2ccccn2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 13, 13, 13, 13, 14, 14, 14, 23, 23, 23, 23, 23, 13, 13, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 13, 13, 13, 13, 13, 23, 23, 23, 23, 13, 13, 13, 13, 7, 7, 7, 7] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486777 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486777/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486777 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 395) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/395 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/395' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCN(S(=O)(=O)c2ccccn2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486777.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486777/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184486777 none O=C(NC1CCN(S(=O)(=O)c2ccccn2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 12, 12, 12, 12, 13, 13, 13, 23, 23, 23, 23, 23, 12, 12, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 12, 12, 12, 12, 12, 23, 23, 23, 23, 12, 12, 12, 12, 7, 7, 7, 7] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486777 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184486777 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486777/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486777/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486777 Building ZINC001184486777 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486777' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486777 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486777 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486777/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486777 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 394) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/394: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCN(S(=O)(=O)c2ccccn2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486777.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184486777 none O=C(NC1CCN(S(=O)(=O)c2ccccn2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 13, 13, 13, 13, 14, 14, 14, 23, 23, 23, 23, 23, 13, 13, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 13, 13, 13, 13, 13, 23, 23, 23, 23, 13, 13, 13, 13, 7, 7, 7, 7] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486777 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486777/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486777 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 395) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/395: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCN(S(=O)(=O)c2ccccn2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486777.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486777/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184486777 none O=C(NC1CCN(S(=O)(=O)c2ccccn2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 12, 12, 12, 12, 13, 13, 13, 23, 23, 23, 23, 23, 12, 12, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 12, 12, 12, 12, 12, 23, 23, 23, 23, 12, 12, 12, 12, 7, 7, 7, 7] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486777 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184486777 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486777/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486777/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184486777 Building ZINC001184487354 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487354' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487354 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487354 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487354/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487354 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 396) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/396 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/396' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCS(=O)(=O)CC1) `ZINC001184487354.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001184487354 none COCCC1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 24, 16, 9, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 16, 16, 16, 16, 16, 16, 16, 33, 33, 33, 25, 25, 24, 24, 4, 6, 6, 6, 6, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 113 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487354 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487354/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487354 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 397) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/397 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/397' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCS(=O)(=O)CC1) `ZINC001184487354.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487354/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001184487354 none COCCC1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 15, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 15, 28, 28, 28, 23, 23, 23, 23, 4, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 98 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487354 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184487354 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487354/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487354/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487354 Building ZINC001184487354 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487354' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487354 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487354 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487354/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487354 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 396) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COCCC1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCS(=O)(=O)CC1) `ZINC001184487354.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001184487354 none COCCC1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 24, 16, 9, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 16, 16, 16, 16, 16, 16, 16, 33, 33, 33, 25, 25, 24, 24, 4, 6, 6, 6, 6, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 113 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487354 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487354/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487354 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 397) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COCCC1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCS(=O)(=O)CC1) `ZINC001184487354.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487354/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001184487354 none COCCC1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CCS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 15, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 15, 28, 28, 28, 23, 23, 23, 23, 4, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 98 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487354 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184487354 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487354/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487354/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487354 Building ZINC001184487474 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487474' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487474 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487474 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487474/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487474 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 398) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/398 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/398' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cnc2nc(SC)nn2c1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21) `ZINC001184487474.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184487474 none CCOC(=O)c1cnc2nc(SC)nn2c1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'S.3', 'C.3', 'N.2', 'N.pl3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 1, 8, 1, 14, 5, 8, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 9, 7, 9, 7, 7, 7, 7, 7, 7, 7, 19, 7, 7, 7, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 9, 6, 6, 13, 13, 13, 13, 13, 7, 19, 19, 19, 7, 6, 6, 6, 9, 9, 9, 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487474 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487474/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487474 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 399) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/399 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/399' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cnc2nc(SC)nn2c1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21) `ZINC001184487474.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487474/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184487474 none CCOC(=O)c1cnc2nc(SC)nn2c1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'S.3', 'C.3', 'N.2', 'N.pl3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 1, 8, 1, 14, 5, 8, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 9, 7, 9, 7, 7, 7, 7, 7, 7, 7, 19, 7, 7, 7, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 9, 6, 6, 13, 13, 13, 13, 13, 7, 19, 19, 19, 7, 6, 6, 6, 9, 9, 9, 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487474 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184487474 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487474/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487474/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487474 Building ZINC001184487474 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487474' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487474 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487474 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487474/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487474 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 398) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCOC(=O)c1cnc2nc(SC)nn2c1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21) `ZINC001184487474.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184487474 none CCOC(=O)c1cnc2nc(SC)nn2c1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'S.3', 'C.3', 'N.2', 'N.pl3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 1, 8, 1, 14, 5, 8, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 9, 7, 9, 7, 7, 7, 7, 7, 7, 7, 19, 7, 7, 7, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 9, 6, 6, 13, 13, 13, 13, 13, 7, 19, 19, 19, 7, 6, 6, 6, 9, 9, 9, 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487474 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487474/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487474 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 399) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCOC(=O)c1cnc2nc(SC)nn2c1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21) `ZINC001184487474.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487474/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184487474 none CCOC(=O)c1cnc2nc(SC)nn2c1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'S.3', 'C.3', 'N.2', 'N.pl3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 1, 8, 1, 14, 5, 8, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 9, 7, 9, 7, 7, 7, 7, 7, 7, 7, 19, 7, 7, 7, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 9, 6, 6, 13, 13, 13, 13, 13, 7, 19, 19, 19, 7, 6, 6, 6, 9, 9, 9, 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487474 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184487474 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487474/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487474/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487474 Building ZINC001184487672 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487672' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487672 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487672 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487672/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487672 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 400) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/400 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/400' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1)N1CCOCC1) `ZINC001184487672.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001184487672 none O=C(NC1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1)N1CCOCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 8, 5, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 2, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 19, 21, 21, 21, 21, 21, 19, 8, 8, 8, 8, 8, 5, 5, 5, 5, 8, 8, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21] 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: 62 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487672 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487672/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487672 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 401) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/401 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/401' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1)N1CCOCC1) `ZINC001184487672.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487672/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001184487672 none O=C(NC1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1)N1CCOCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 8, 5, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 6, 2, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 17, 18, 18, 18, 18, 18, 17, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 55 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487672 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184487672 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487672/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487672/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487672 Building ZINC001184487672 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487672' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487672 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487672 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487672/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487672 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 400) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/400: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1)N1CCOCC1) `ZINC001184487672.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001184487672 none O=C(NC1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1)N1CCOCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 8, 5, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 2, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 19, 21, 21, 21, 21, 21, 19, 8, 8, 8, 8, 8, 5, 5, 5, 5, 8, 8, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21] 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: 62 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487672 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487672/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487672 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 401) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/401: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1)N1CCOCC1) `ZINC001184487672.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487672/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001184487672 none O=C(NC1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1)N1CCOCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 8, 5, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 6, 2, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 17, 18, 18, 18, 18, 18, 17, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 55 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487672 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184487672 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487672/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487672/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487672 Building ZINC001184487931 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487931' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487931 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487931 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487931/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487931 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 402) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/402 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/402' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3Cc4nnn(C)c4[C@H](COCc4cccnc4)C3)c2c1) `ZINC001184487931.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184487931 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3Cc4nnn(C)c4[C@H](COCc4cccnc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 8, 8, 5, 1, 5, 7, 5, 12, 5, 1, 1, 1, 1, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 13, 28, 37, 37, 37, 37, 37, 4, 3, 3, 4, 4, 4, 3, 3, 3, 4, 4, 4, 4, 4, 9, 9, 28, 28, 37, 37, 37, 37, 4, 4, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487931 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487931/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487931 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 403) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/403 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/403' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3Cc4nnn(C)c4[C@H](COCc4cccnc4)C3)c2c1) `ZINC001184487931.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487931/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184487931 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3Cc4nnn(C)c4[C@H](COCc4cccnc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 8, 8, 5, 1, 5, 7, 5, 12, 5, 1, 1, 1, 1, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 11, 23, 31, 31, 31, 31, 31, 2, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 6, 6, 23, 23, 31, 31, 31, 31, 2, 2, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487931 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184487931 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487931/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487931/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487931 Building ZINC001184487931 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487931' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487931 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487931 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487931/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487931 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 402) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3Cc4nnn(C)c4[C@H](COCc4cccnc4)C3)c2c1) `ZINC001184487931.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184487931 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3Cc4nnn(C)c4[C@H](COCc4cccnc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 8, 8, 5, 1, 5, 7, 5, 12, 5, 1, 1, 1, 1, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 13, 28, 37, 37, 37, 37, 37, 4, 3, 3, 4, 4, 4, 3, 3, 3, 4, 4, 4, 4, 4, 9, 9, 28, 28, 37, 37, 37, 37, 4, 4, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487931 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487931/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487931 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 403) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3Cc4nnn(C)c4[C@H](COCc4cccnc4)C3)c2c1) `ZINC001184487931.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487931/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184487931 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3Cc4nnn(C)c4[C@H](COCc4cccnc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 8, 8, 5, 1, 5, 7, 5, 12, 5, 1, 1, 1, 1, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 11, 23, 31, 31, 31, 31, 31, 2, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 6, 6, 23, 23, 31, 31, 31, 31, 2, 2, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487931 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184487931 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487931/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487931/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487931 Building ZINC001184487932 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487932' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487932 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487932 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487932/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487932 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 404) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/404 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/404' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3Cc4nnn(C)c4[C@@H](COCc4cccnc4)C3)c2c1) `ZINC001184487932.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184487932 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3Cc4nnn(C)c4[C@@H](COCc4cccnc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 8, 8, 5, 1, 5, 7, 5, 12, 5, 1, 1, 1, 1, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 11, 23, 31, 31, 31, 31, 31, 2, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 6, 6, 23, 23, 31, 31, 31, 31, 2, 2, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487932 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487932/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487932 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 405) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/405 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/405' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3Cc4nnn(C)c4[C@@H](COCc4cccnc4)C3)c2c1) `ZINC001184487932.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487932/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184487932 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3Cc4nnn(C)c4[C@@H](COCc4cccnc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 8, 8, 5, 1, 5, 7, 5, 12, 5, 1, 1, 1, 1, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 3, 3, 3, 8, 12, 25, 35, 35, 35, 35, 35, 3, 3, 3, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 25, 25, 35, 35, 35, 35, 3, 3, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487932 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184487932 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487932/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487932/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487932 Building ZINC001184487932 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487932' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487932 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487932 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487932/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487932 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 404) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3Cc4nnn(C)c4[C@@H](COCc4cccnc4)C3)c2c1) `ZINC001184487932.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184487932 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3Cc4nnn(C)c4[C@@H](COCc4cccnc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 8, 8, 5, 1, 5, 7, 5, 12, 5, 1, 1, 1, 1, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 11, 23, 31, 31, 31, 31, 31, 2, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 6, 6, 23, 23, 31, 31, 31, 31, 2, 2, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487932 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487932/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487932 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 405) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3Cc4nnn(C)c4[C@@H](COCc4cccnc4)C3)c2c1) `ZINC001184487932.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487932/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184487932 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3Cc4nnn(C)c4[C@@H](COCc4cccnc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 8, 8, 5, 1, 5, 7, 5, 12, 5, 1, 1, 1, 1, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 3, 3, 3, 8, 12, 25, 35, 35, 35, 35, 35, 3, 3, 3, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 25, 25, 35, 35, 35, 35, 3, 3, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487932 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184487932 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487932/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487932/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487932 Building ZINC001184487941 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487941' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487941 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487941 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487941/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487941 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 406) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/406 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/406' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(c3nc(N4CCOCC4)nc4c3CCNCC4)C(C)C)c2c1) `ZINC001184487941.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487941/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184487941 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(c3nc(N4CCOCC4)nc4c3CCNCC4)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', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 8, 5, 5, 12, 5, 5, 8, 1, 1, 5, 5, 10, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 11, 13, 15, 23, 39, 39, 39, 39, 39, 15, 15, 14, 15, 15, 15, 15, 15, 9, 18, 18, 4, 4, 7, 7, 7, 4, 4, 4, 39, 39, 39, 39, 39, 39, 39, 39, 15, 15, 15, 15, 15, 15, 15, 15, 15, 18, 18, 18, 18, 18, 18, 18, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 121 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487941 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487941/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487941 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 407) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/407 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/407' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(c3nc(N4CCOCC4)nc4c3CCNCC4)C(C)C)c2c1) `ZINC001184487941.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487941/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184487941 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(c3nc(N4CCOCC4)nc4c3CCNCC4)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', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 8, 5, 5, 12, 5, 5, 8, 1, 1, 5, 5, 10, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 11, 13, 16, 23, 40, 40, 40, 40, 40, 15, 16, 14, 16, 16, 16, 16, 16, 9, 16, 16, 4, 4, 7, 7, 7, 4, 4, 4, 40, 40, 40, 40, 40, 40, 40, 40, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 17, 17, 16, 17, 17, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487941 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184487941 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487941/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487941/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487941 Building ZINC001184487941 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487941' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487941 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487941 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487941/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487941 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 406) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(c3nc(N4CCOCC4)nc4c3CCNCC4)C(C)C)c2c1) `ZINC001184487941.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487941/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184487941 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(c3nc(N4CCOCC4)nc4c3CCNCC4)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', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 8, 5, 5, 12, 5, 5, 8, 1, 1, 5, 5, 10, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 11, 13, 15, 23, 39, 39, 39, 39, 39, 15, 15, 14, 15, 15, 15, 15, 15, 9, 18, 18, 4, 4, 7, 7, 7, 4, 4, 4, 39, 39, 39, 39, 39, 39, 39, 39, 15, 15, 15, 15, 15, 15, 15, 15, 15, 18, 18, 18, 18, 18, 18, 18, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 121 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487941 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487941/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487941 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 407) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(c3nc(N4CCOCC4)nc4c3CCNCC4)C(C)C)c2c1) `ZINC001184487941.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487941/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184487941 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(c3nc(N4CCOCC4)nc4c3CCNCC4)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', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 8, 5, 5, 12, 5, 5, 8, 1, 1, 5, 5, 10, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 11, 13, 16, 23, 40, 40, 40, 40, 40, 15, 16, 14, 16, 16, 16, 16, 16, 9, 16, 16, 4, 4, 7, 7, 7, 4, 4, 4, 40, 40, 40, 40, 40, 40, 40, 40, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 17, 17, 16, 17, 17, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487941 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184487941 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487941/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487941/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184487941 Building ZINC001184488145 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488145' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488145 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184488145 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488145/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488145 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 408) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/408 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/408' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)C(F)(F)Br) `ZINC001184488145.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184488145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001184488145 none O=C(NCCNC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)C(F)(F)Br NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 15, 15, 17, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 9, 9, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 17, 31, 31, 31, 17, 9, 9, 9, 9, 3, 4, 4, 4, 4] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488145 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488145/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488145 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 409) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/409 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/409' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)C(F)(F)Br) `ZINC001184488145.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184488145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488145/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001184488145 none O=C(NCCNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)C(F)(F)Br NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 15, 15, 17, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 9, 9, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 17, 31, 31, 31, 17, 9, 9, 9, 9, 3, 4, 4, 4, 4] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488145 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184488145 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488145/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488145/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488145 Building ZINC001184488145 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488145' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488145 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184488145 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488145/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488145 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 408) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/408: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)C(F)(F)Br) `ZINC001184488145.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184488145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001184488145 none O=C(NCCNC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)C(F)(F)Br NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 15, 15, 17, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 9, 9, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 17, 31, 31, 31, 17, 9, 9, 9, 9, 3, 4, 4, 4, 4] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488145 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488145/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488145 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 409) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/409: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)C(F)(F)Br) `ZINC001184488145.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184488145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488145/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001184488145 none O=C(NCCNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)C(F)(F)Br NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 15, 15, 17, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 9, 9, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 17, 31, 31, 31, 17, 9, 9, 9, 9, 3, 4, 4, 4, 4] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488145 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184488145 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488145/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488145/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488145 Building ZINC001184488621 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488621' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488621 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184488621 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488621/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488621 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 410) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/410 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/410' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(c3ccc(OC)nn3)S(=O)(=O)c3ccc(N)cc3)c2c1) `ZINC001184488621.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184488621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184488621 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(c3ccc(OC)nn3)S(=O)(=O)c3ccc(N)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.3', 'N.ar', 'N.ar', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', '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, 5, 8, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 3, 3, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 9, 22, 22, 22, 22, 22, 22, 22, 9, 18, 18, 18, 28, 28, 18, 18, 28, 28, 5, 5, 7, 7, 7, 5, 5, 5, 22, 22, 22, 22, 22, 28, 28, 28, 28, 28, 28, 5] 40 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488621 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488621/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488621 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 411) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/411 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/411' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(c3ccc(OC)nn3)S(=O)(=O)c3ccc(N)cc3)c2c1) `ZINC001184488621.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184488621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488621/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184488621 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(c3ccc(OC)nn3)S(=O)(=O)c3ccc(N)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.3', 'N.ar', 'N.ar', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', '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, 5, 8, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 3, 3, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 9, 20, 20, 20, 20, 20, 20, 20, 9, 16, 16, 16, 25, 25, 16, 16, 25, 25, 5, 5, 7, 7, 7, 5, 5, 5, 20, 20, 20, 20, 20, 25, 25, 25, 25, 25, 25, 5] 39 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488621 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184488621 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488621/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488621/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488621 Building ZINC001184488621 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488621' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488621 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184488621 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488621/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488621 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 410) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(c3ccc(OC)nn3)S(=O)(=O)c3ccc(N)cc3)c2c1) `ZINC001184488621.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184488621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184488621 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(c3ccc(OC)nn3)S(=O)(=O)c3ccc(N)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.3', 'N.ar', 'N.ar', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', '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, 5, 8, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 3, 3, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 9, 22, 22, 22, 22, 22, 22, 22, 9, 18, 18, 18, 28, 28, 18, 18, 28, 28, 5, 5, 7, 7, 7, 5, 5, 5, 22, 22, 22, 22, 22, 28, 28, 28, 28, 28, 28, 5] 40 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488621 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488621/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488621 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 411) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(c3ccc(OC)nn3)S(=O)(=O)c3ccc(N)cc3)c2c1) `ZINC001184488621.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184488621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488621/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184488621 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(c3ccc(OC)nn3)S(=O)(=O)c3ccc(N)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.3', 'N.ar', 'N.ar', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', '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, 5, 8, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 3, 3, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 9, 20, 20, 20, 20, 20, 20, 20, 9, 16, 16, 16, 25, 25, 16, 16, 25, 25, 5, 5, 7, 7, 7, 5, 5, 5, 20, 20, 20, 20, 20, 25, 25, 25, 25, 25, 25, 5] 39 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488621 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184488621 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488621/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488621/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488621 Building ZINC001184488958 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488958' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488958 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184488958 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488958/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488958 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 412) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/412 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/412' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)c1ccc(O)c(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c1) `ZINC001184488958.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184488958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001184488958 none CNS(=O)(=O)c1ccc(O)c(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 8, 14, 11, 11, 1, 1, 1, 1, 12, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 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] 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: [23, 17, 12, 17, 17, 12, 9, 12, 12, 12, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 12, 23, 23, 23, 23, 12, 12, 24, 4, 9, 9, 9, 9, 12] 100 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488958 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488958/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488958 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 413) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/413 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/413' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)c1ccc(O)c(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c1) `ZINC001184488958.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184488958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488958/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001184488958 none CNS(=O)(=O)c1ccc(O)c(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 8, 14, 11, 11, 1, 1, 1, 1, 12, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 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] 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, 17, 12, 17, 17, 12, 5, 12, 12, 12, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 12, 22, 22, 22, 22, 12, 12, 24, 4, 9, 9, 9, 9, 12] 100 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488958 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184488958 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488958/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488958/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488958 Building ZINC001184488958 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488958' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488958 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184488958 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488958/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488958 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 412) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CNS(=O)(=O)c1ccc(O)c(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c1) `ZINC001184488958.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184488958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001184488958 none CNS(=O)(=O)c1ccc(O)c(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 8, 14, 11, 11, 1, 1, 1, 1, 12, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 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] 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: [23, 17, 12, 17, 17, 12, 9, 12, 12, 12, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 12, 23, 23, 23, 23, 12, 12, 24, 4, 9, 9, 9, 9, 12] 100 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488958 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488958/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488958 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 413) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CNS(=O)(=O)c1ccc(O)c(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c1) `ZINC001184488958.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184488958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488958/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001184488958 none CNS(=O)(=O)c1ccc(O)c(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 8, 14, 11, 11, 1, 1, 1, 1, 12, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 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] 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, 17, 12, 17, 17, 12, 5, 12, 12, 12, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 12, 22, 22, 22, 22, 12, 12, 24, 4, 9, 9, 9, 9, 12] 100 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488958 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184488958 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488958/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488958/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184488958 Building ZINC001184489015 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489015' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489015 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489015 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489015/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489015 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 414) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/414 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/414' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3C[C@@H]4COC[C@H](C(=O)N5CCC(F)CC5)[C@@H]4C3)c2c1) `ZINC001184489015.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489015/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184489015 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3C[C@@H]4COC[C@H](C(=O)N5CCC(F)CC5)[C@@H]4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 15, 5, 5, 5, 7, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 11, 22, 29, 29, 29, 29, 29, 29, 29, 9, 9, 9, 4, 4, 7, 7, 7, 4, 4, 4, 9, 9, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 9, 9, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 70 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489015 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489015/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489015 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 415) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/415 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/415' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3C[C@@H]4COC[C@H](C(=O)N5CCC(F)CC5)[C@@H]4C3)c2c1) `ZINC001184489015.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489015/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184489015 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3C[C@@H]4COC[C@H](C(=O)N5CCC(F)CC5)[C@@H]4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 15, 5, 5, 5, 7, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 9, 18, 23, 25, 25, 25, 25, 25, 25, 8, 8, 8, 5, 5, 8, 8, 8, 5, 5, 5, 8, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 64 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489015 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184489015 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489015/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489015/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489015 Building ZINC001184489015 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489015' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489015 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489015 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489015/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489015 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 414) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3C[C@@H]4COC[C@H](C(=O)N5CCC(F)CC5)[C@@H]4C3)c2c1) `ZINC001184489015.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489015/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184489015 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3C[C@@H]4COC[C@H](C(=O)N5CCC(F)CC5)[C@@H]4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 15, 5, 5, 5, 7, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 11, 22, 29, 29, 29, 29, 29, 29, 29, 9, 9, 9, 4, 4, 7, 7, 7, 4, 4, 4, 9, 9, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 9, 9, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 70 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489015 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489015/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489015 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 415) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3C[C@@H]4COC[C@H](C(=O)N5CCC(F)CC5)[C@@H]4C3)c2c1) `ZINC001184489015.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489015/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184489015 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3C[C@@H]4COC[C@H](C(=O)N5CCC(F)CC5)[C@@H]4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 15, 5, 5, 5, 7, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 9, 18, 23, 25, 25, 25, 25, 25, 25, 8, 8, 8, 5, 5, 8, 8, 8, 5, 5, 5, 8, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 64 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489015 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184489015 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489015/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489015/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489015 Building ZINC001184489299 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489299' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489299 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489299 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489299/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489299 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 416) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/416 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/416' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN2C(=O)N[C@@]3(CCN(C(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)C3)C2=O)cc1) `ZINC001184489299.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184489299 none COc1ccc(CN2C(=O)N[C@@]3(CCN(C(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)C3)C2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 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, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 25, 25, 19, 6, 6, 6, 6, 6, 6, 6, 6, 2, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 7, 4, 4, 6, 6, 6, 25, 25, 25, 25, 25, 25, 25, 19, 19, 6, 6, 6, 6, 6, 4, 4, 4, 7, 7, 7, 4, 6, 6, 25, 25] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489299 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489299/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489299 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 417) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/417 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/417' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN2C(=O)N[C@@]3(CCN(C(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)C3)C2=O)cc1) `ZINC001184489299.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489299/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184489299 none COc1ccc(CN2C(=O)N[C@@]3(CCN(C(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)C3)C2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 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, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 29, 29, 21, 5, 5, 5, 5, 5, 5, 5, 5, 2, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 5, 3, 3, 5, 5, 5, 29, 29, 29, 29, 29, 29, 29, 21, 21, 5, 5, 5, 5, 5, 3, 3, 3, 5, 5, 5, 3, 5, 5, 29, 29] 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: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489299 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184489299 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489299/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489299/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489299 Building ZINC001184489299 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489299' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489299 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489299 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489299/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489299 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 416) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc(CN2C(=O)N[C@@]3(CCN(C(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)C3)C2=O)cc1) `ZINC001184489299.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184489299 none COc1ccc(CN2C(=O)N[C@@]3(CCN(C(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)C3)C2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 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, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 25, 25, 19, 6, 6, 6, 6, 6, 6, 6, 6, 2, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 7, 4, 4, 6, 6, 6, 25, 25, 25, 25, 25, 25, 25, 19, 19, 6, 6, 6, 6, 6, 4, 4, 4, 7, 7, 7, 4, 6, 6, 25, 25] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489299 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489299/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489299 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 417) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc(CN2C(=O)N[C@@]3(CCN(C(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)C3)C2=O)cc1) `ZINC001184489299.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489299/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184489299 none COc1ccc(CN2C(=O)N[C@@]3(CCN(C(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)C3)C2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 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, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 29, 29, 21, 5, 5, 5, 5, 5, 5, 5, 5, 2, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 5, 3, 3, 5, 5, 5, 29, 29, 29, 29, 29, 29, 29, 21, 21, 5, 5, 5, 5, 5, 3, 3, 3, 5, 5, 5, 3, 5, 5, 29, 29] 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: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489299 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184489299 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489299/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489299/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489299 Building ZINC001184489300 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489300' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489300 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489300 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489300/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489300 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 418) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/418 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/418' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN2C(=O)N[C@]3(CCN(C(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)C3)C2=O)cc1) `ZINC001184489300.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184489300 none COc1ccc(CN2C(=O)N[C@]3(CCN(C(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)C3)C2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 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, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 29, 29, 21, 5, 5, 5, 5, 5, 5, 5, 5, 2, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 5, 3, 3, 5, 5, 5, 29, 29, 29, 29, 29, 29, 29, 21, 21, 5, 5, 5, 5, 5, 3, 3, 3, 5, 5, 5, 3, 5, 5, 29, 29] 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: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489300 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489300/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489300 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 419) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/419 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/419' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN2C(=O)N[C@]3(CCN(C(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)C3)C2=O)cc1) `ZINC001184489300.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489300/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184489300 none COc1ccc(CN2C(=O)N[C@]3(CCN(C(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)C3)C2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 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, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 24, 18, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 6, 4, 4, 5, 5, 5, 24, 24, 24, 24, 24, 24, 24, 18, 18, 5, 5, 5, 5, 5, 4, 4, 4, 6, 6, 6, 4, 5, 5, 24, 24] 50 rigid atoms, others: [17, 18, 19, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489300 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184489300 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489300/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489300/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489300 Building ZINC001184489300 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489300' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489300 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489300 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489300/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489300 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 418) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc(CN2C(=O)N[C@]3(CCN(C(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)C3)C2=O)cc1) `ZINC001184489300.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184489300 none COc1ccc(CN2C(=O)N[C@]3(CCN(C(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)C3)C2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 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, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 29, 29, 21, 5, 5, 5, 5, 5, 5, 5, 5, 2, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 5, 3, 3, 5, 5, 5, 29, 29, 29, 29, 29, 29, 29, 21, 21, 5, 5, 5, 5, 5, 3, 3, 3, 5, 5, 5, 3, 5, 5, 29, 29] 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: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489300 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489300/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489300 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 419) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc(CN2C(=O)N[C@]3(CCN(C(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)C3)C2=O)cc1) `ZINC001184489300.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489300/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184489300 none COc1ccc(CN2C(=O)N[C@]3(CCN(C(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)C3)C2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 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, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 24, 18, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 6, 4, 4, 5, 5, 5, 24, 24, 24, 24, 24, 24, 24, 18, 18, 5, 5, 5, 5, 5, 4, 4, 4, 6, 6, 6, 4, 5, 5, 24, 24] 50 rigid atoms, others: [17, 18, 19, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489300 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184489300 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489300/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489300/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489300 Building ZINC001184489487 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489487' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489487 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489487 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489487/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489487 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 420) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/420 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/420' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCO[C@]4(CCCN(C(=O)c5ccco5)C4)C3)c2c1) `ZINC001184489487.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489487/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489487 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCO[C@]4(CCCN(C(=O)c5ccco5)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.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 3, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 21, 21, 30, 30, 30, 30, 11, 11, 4, 4, 5, 5, 5, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 30, 30, 30, 11, 11, 11, 11, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489487 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489487/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489487 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 421) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/421 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/421' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCO[C@]4(CCCN(C(=O)c5ccco5)C4)C3)c2c1) `ZINC001184489487.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489487/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489487 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCO[C@]4(CCCN(C(=O)c5ccco5)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.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 26, 26, 31, 31, 31, 31, 13, 13, 4, 4, 5, 5, 5, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 31, 31, 31, 13, 13, 13, 13, 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489487 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184489487 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489487/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489487/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489487 Building ZINC001184489487 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489487' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489487 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489487 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489487/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489487 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 420) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCO[C@]4(CCCN(C(=O)c5ccco5)C4)C3)c2c1) `ZINC001184489487.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489487/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489487 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCO[C@]4(CCCN(C(=O)c5ccco5)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.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 3, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 21, 21, 30, 30, 30, 30, 11, 11, 4, 4, 5, 5, 5, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 30, 30, 30, 11, 11, 11, 11, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489487 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489487/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489487 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 421) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCO[C@]4(CCCN(C(=O)c5ccco5)C4)C3)c2c1) `ZINC001184489487.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489487/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489487 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCO[C@]4(CCCN(C(=O)c5ccco5)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.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 26, 26, 31, 31, 31, 31, 13, 13, 4, 4, 5, 5, 5, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 31, 31, 31, 13, 13, 13, 13, 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489487 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184489487 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489487/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489487/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489487 Building ZINC001184489488 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489488' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489488 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489488 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489488/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489488 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 422) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/422 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/422' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCO[C@@]4(CCCN(C(=O)c5ccco5)C4)C3)c2c1) `ZINC001184489488.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489488 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCO[C@@]4(CCCN(C(=O)c5ccco5)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.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 4, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 29, 29, 36, 36, 36, 36, 14, 14, 5, 5, 7, 7, 7, 5, 5, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 36, 36, 36, 14, 14, 14, 14, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489488 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489488/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489488 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 423) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/423 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/423' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCO[C@@]4(CCCN(C(=O)c5ccco5)C4)C3)c2c1) `ZINC001184489488.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489488/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489488 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCO[C@@]4(CCCN(C(=O)c5ccco5)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.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 4, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 21, 21, 30, 30, 30, 30, 13, 13, 4, 4, 6, 6, 6, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 30, 30, 30, 13, 13, 13, 13, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489488 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184489488 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489488/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489488/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489488 Building ZINC001184489488 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489488' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489488 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489488 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489488/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489488 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 422) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCO[C@@]4(CCCN(C(=O)c5ccco5)C4)C3)c2c1) `ZINC001184489488.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489488 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCO[C@@]4(CCCN(C(=O)c5ccco5)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.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 4, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 29, 29, 36, 36, 36, 36, 14, 14, 5, 5, 7, 7, 7, 5, 5, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 36, 36, 36, 14, 14, 14, 14, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489488 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489488/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489488 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 423) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCO[C@@]4(CCCN(C(=O)c5ccco5)C4)C3)c2c1) `ZINC001184489488.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489488/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489488 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCO[C@@]4(CCCN(C(=O)c5ccco5)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.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 4, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 21, 21, 30, 30, 30, 30, 13, 13, 4, 4, 6, 6, 6, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 30, 30, 30, 13, 13, 13, 13, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489488 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184489488 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489488/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489488/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489488 Building ZINC001184489498 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489498' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489498 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489498 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489498/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489498 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 424) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/424 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/424' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3C[C@@H]4COC[C@]4(C(=O)NCCc4ccccc4)C3)c2c1) `ZINC001184489498.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184489498 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3C[C@@H]4COC[C@]4(C(=O)NCCc4ccccc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.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.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 11, 11, 11, 33, 45, 45, 45, 45, 45, 45, 7, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 11, 33, 33, 45, 45, 45, 45, 45, 45, 45, 7, 7, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489498 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489498/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489498 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 425) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/425 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/425' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3C[C@@H]4COC[C@]4(C(=O)NCCc4ccccc4)C3)c2c1) `ZINC001184489498.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489498/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184489498 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3C[C@@H]4COC[C@]4(C(=O)NCCc4ccccc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.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.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 23, 31, 31, 31, 31, 31, 31, 4, 3, 3, 4, 4, 4, 3, 3, 3, 4, 4, 4, 4, 4, 4, 6, 23, 23, 31, 31, 31, 31, 31, 31, 31, 4, 4, 3] 50 rigid atoms, others: [9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489498 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184489498 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489498/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489498/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489498 Building ZINC001184489498 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489498' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489498 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489498 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489498/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489498 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 424) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3C[C@@H]4COC[C@]4(C(=O)NCCc4ccccc4)C3)c2c1) `ZINC001184489498.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184489498 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3C[C@@H]4COC[C@]4(C(=O)NCCc4ccccc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.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.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 11, 11, 11, 33, 45, 45, 45, 45, 45, 45, 7, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 11, 33, 33, 45, 45, 45, 45, 45, 45, 45, 7, 7, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489498 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489498/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489498 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 425) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3C[C@@H]4COC[C@]4(C(=O)NCCc4ccccc4)C3)c2c1) `ZINC001184489498.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489498/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184489498 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3C[C@@H]4COC[C@]4(C(=O)NCCc4ccccc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.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.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 23, 31, 31, 31, 31, 31, 31, 4, 3, 3, 4, 4, 4, 3, 3, 3, 4, 4, 4, 4, 4, 4, 6, 23, 23, 31, 31, 31, 31, 31, 31, 31, 4, 4, 3] 50 rigid atoms, others: [9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489498 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184489498 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489498/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489498/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489498 Building ZINC001184489515 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489515' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489515 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489515 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489515/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489515 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 426) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/426 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/426' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4O[C@H](C(=O)N(C)Cc5ccccn5)C[C@H]43)c2c1) `ZINC001184489515.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489515 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4O[C@H](C(=O)N(C)Cc5ccccn5)C[C@H]43)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 7, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 8, 5, 5, 7, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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] 0 hydrogens need 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, 2, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 17, 17, 35, 40, 40, 40, 40, 40, 4, 4, 4, 4, 4, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 17, 17, 17, 35, 35, 40, 40, 40, 40, 4, 4, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489515 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489515/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489515 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 427) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/427 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/427' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4O[C@H](C(=O)N(C)Cc5ccccn5)C[C@H]43)c2c1) `ZINC001184489515.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489515/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489515 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4O[C@H](C(=O)N(C)Cc5ccccn5)C[C@H]43)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 7, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 8, 5, 5, 7, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 12, 12, 27, 27, 27, 27, 27, 27, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 12, 12, 12, 27, 27, 27, 27, 27, 27, 4, 4, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489515 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184489515 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489515/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489515/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489515 Building ZINC001184489515 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489515' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489515 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489515 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489515/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489515 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 426) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4O[C@H](C(=O)N(C)Cc5ccccn5)C[C@H]43)c2c1) `ZINC001184489515.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489515 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4O[C@H](C(=O)N(C)Cc5ccccn5)C[C@H]43)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 7, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 8, 5, 5, 7, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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] 0 hydrogens need 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, 2, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 17, 17, 35, 40, 40, 40, 40, 40, 4, 4, 4, 4, 4, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 17, 17, 17, 35, 35, 40, 40, 40, 40, 4, 4, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489515 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489515/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489515 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 427) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4O[C@H](C(=O)N(C)Cc5ccccn5)C[C@H]43)c2c1) `ZINC001184489515.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489515/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489515 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4O[C@H](C(=O)N(C)Cc5ccccn5)C[C@H]43)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 7, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 8, 5, 5, 7, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 12, 12, 27, 27, 27, 27, 27, 27, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 12, 12, 12, 27, 27, 27, 27, 27, 27, 4, 4, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489515 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184489515 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489515/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489515/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489515 Building ZINC001184489702 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489702' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489702 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489702 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489702/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489702 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 428) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/428 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/428' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4OC[C@@H](C(=O)NCCc5ccccn5)C[C@H]4C3)c2c1) `ZINC001184489702.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489702/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001184489702 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4OC[C@@H](C(=O)NCCc5ccccn5)C[C@H]4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 7, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 8, 5, 5, 7, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 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] 0 hydrogens need 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 19, 25, 25, 25, 25, 25, 1, 1, 1, 1, 5, 5, 6, 6, 6, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 14, 14, 19, 19, 25, 25, 25, 25, 1, 1, 1, 1, 5] 50 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 34, 35, 36, 37, 46, 47, 48, 49, 50, 51, 61, 62, 63, 64] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 52, 53, 54, 55, 56, 57, 58, 59, 60, 65]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489702 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489702/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489702 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 429) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/429 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/429' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4OC[C@@H](C(=O)NCCc5ccccn5)C[C@H]4C3)c2c1) `ZINC001184489702.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489702/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001184489702 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4OC[C@@H](C(=O)NCCc5ccccn5)C[C@H]4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 7, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 8, 5, 5, 7, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 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] 0 hydrogens need 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, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 13, 23, 31, 31, 31, 31, 31, 2, 2, 2, 2, 3, 3, 5, 5, 5, 3, 3, 3, 2, 2, 2, 2, 2, 2, 4, 13, 13, 23, 23, 31, 31, 31, 31, 2, 2, 2, 2, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489702 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184489702 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489702/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489702/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489702 Building ZINC001184489702 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489702' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489702 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489702 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489702/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489702 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 428) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4OC[C@@H](C(=O)NCCc5ccccn5)C[C@H]4C3)c2c1) `ZINC001184489702.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489702/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001184489702 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4OC[C@@H](C(=O)NCCc5ccccn5)C[C@H]4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 7, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 8, 5, 5, 7, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 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] 0 hydrogens need 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 19, 25, 25, 25, 25, 25, 1, 1, 1, 1, 5, 5, 6, 6, 6, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 14, 14, 19, 19, 25, 25, 25, 25, 1, 1, 1, 1, 5] 50 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 34, 35, 36, 37, 46, 47, 48, 49, 50, 51, 61, 62, 63, 64] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 52, 53, 54, 55, 56, 57, 58, 59, 60, 65]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489702 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489702/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489702 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 429) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4OC[C@@H](C(=O)NCCc5ccccn5)C[C@H]4C3)c2c1) `ZINC001184489702.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489702/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001184489702 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4OC[C@@H](C(=O)NCCc5ccccn5)C[C@H]4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 7, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 8, 5, 5, 7, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 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] 0 hydrogens need 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, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 13, 23, 31, 31, 31, 31, 31, 2, 2, 2, 2, 3, 3, 5, 5, 5, 3, 3, 3, 2, 2, 2, 2, 2, 2, 4, 13, 13, 23, 23, 31, 31, 31, 31, 2, 2, 2, 2, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489702 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184489702 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489702/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489702/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489702 Building ZINC001184489734 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489734' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489734 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489734 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489734/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489734 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 430) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/430 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/430' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)c1ccc2c(c1)C1(CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(OC)cc43)CC1)C(=O)N2) `ZINC001184489734.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184489734 none CNC(=O)c1ccc2c(c1)C1(CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(OC)cc43)CC1)C(=O)N2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 1, 11, 8, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 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: [27, 27, 16, 27, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 2, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 9, 6, 6, 16, 16, 16, 16, 16, 27, 27, 27, 27, 16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 9, 9, 9, 6, 16, 16, 16, 16, 16] 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]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489734 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489734/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489734 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 431) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/431 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/431' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)c1ccc2c(c1)C1(CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(OC)cc43)CC1)C(=O)N2) `ZINC001184489734.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489734/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184489734 none CNC(=O)c1ccc2c(c1)C1(CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(OC)cc43)CC1)C(=O)N2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 1, 11, 8, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 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: [25, 25, 16, 25, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 2, 8, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 9, 6, 6, 16, 16, 16, 16, 16, 25, 25, 25, 25, 16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 9, 9, 9, 6, 16, 16, 16, 16, 16] 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489734 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184489734 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489734/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489734/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489734 Building ZINC001184489734 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489734' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489734 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489734 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489734/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489734 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 430) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CNC(=O)c1ccc2c(c1)C1(CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(OC)cc43)CC1)C(=O)N2) `ZINC001184489734.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184489734 none CNC(=O)c1ccc2c(c1)C1(CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(OC)cc43)CC1)C(=O)N2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 1, 11, 8, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 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: [27, 27, 16, 27, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 2, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 9, 6, 6, 16, 16, 16, 16, 16, 27, 27, 27, 27, 16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 9, 9, 9, 6, 16, 16, 16, 16, 16] 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]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489734 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489734/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489734 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 431) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CNC(=O)c1ccc2c(c1)C1(CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(OC)cc43)CC1)C(=O)N2) `ZINC001184489734.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489734/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184489734 none CNC(=O)c1ccc2c(c1)C1(CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(OC)cc43)CC1)C(=O)N2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 1, 11, 8, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 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: [25, 25, 16, 25, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 2, 8, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 9, 6, 6, 16, 16, 16, 16, 16, 25, 25, 25, 25, 16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 9, 9, 9, 6, 16, 16, 16, 16, 16] 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489734 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184489734 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489734/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489734/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489734 Building ZINC001184489739 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184489739 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 432) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/432 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/432' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCCN4Cc3ccccc3)c2c1) `ZINC001184489739.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489739 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCCN4Cc3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 18, 21, 22, 22, 22, 21, 22, 22, 22, 22, 22, 22, 22, 23, 25, 25, 23, 25, 25, 6, 6, 7, 7, 7, 6, 6, 6, 22, 22, 22, 22, 21, 22, 22, 22, 22, 22, 22, 22, 22, 23, 23, 25, 25, 25, 25, 25, 6] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 69 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 433) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/433 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/433' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCCN4Cc3ccccc3)c2c1) `ZINC001184489739.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489739 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCCN4Cc3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 15, 21, 23, 23, 23, 22, 23, 23, 23, 23, 23, 23, 23, 24, 26, 26, 26, 26, 26, 4, 4, 6, 6, 6, 4, 4, 4, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 24, 24, 26, 26, 26, 26, 26, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 65 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 434) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/434 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/434' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCCN4Cc3ccccc3)c2c1) `ZINC001184489739.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184489739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489739 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCCN4Cc3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 18, 21, 22, 22, 22, 21, 22, 22, 22, 22, 22, 22, 22, 23, 25, 25, 23, 25, 25, 6, 6, 7, 7, 7, 6, 6, 6, 22, 22, 22, 22, 21, 22, 22, 22, 22, 22, 22, 22, 22, 23, 23, 25, 25, 25, 25, 25, 6] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 69 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 435) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/435 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/435' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCCN4Cc3ccccc3)c2c1) `ZINC001184489739.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184489739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489739 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCCN4Cc3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 15, 21, 23, 23, 23, 22, 23, 23, 23, 23, 23, 23, 23, 24, 26, 26, 26, 26, 26, 4, 4, 6, 6, 6, 4, 4, 4, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 24, 24, 26, 26, 26, 26, 26, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 65 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184489739 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739 Building ZINC001184489739 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184489739 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 432) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCCN4Cc3ccccc3)c2c1) `ZINC001184489739.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489739 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCCN4Cc3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 18, 21, 22, 22, 22, 21, 22, 22, 22, 22, 22, 22, 22, 23, 25, 25, 23, 25, 25, 6, 6, 7, 7, 7, 6, 6, 6, 22, 22, 22, 22, 21, 22, 22, 22, 22, 22, 22, 22, 22, 23, 23, 25, 25, 25, 25, 25, 6] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 69 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 433) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCCN4Cc3ccccc3)c2c1) `ZINC001184489739.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489739 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCCN4Cc3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 15, 21, 23, 23, 23, 22, 23, 23, 23, 23, 23, 23, 23, 24, 26, 26, 26, 26, 26, 4, 4, 6, 6, 6, 4, 4, 4, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 24, 24, 26, 26, 26, 26, 26, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 65 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 434) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/434: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCCN4Cc3ccccc3)c2c1) `ZINC001184489739.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184489739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489739 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCCN4Cc3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 18, 21, 22, 22, 22, 21, 22, 22, 22, 22, 22, 22, 22, 23, 25, 25, 23, 25, 25, 6, 6, 7, 7, 7, 6, 6, 6, 22, 22, 22, 22, 21, 22, 22, 22, 22, 22, 22, 22, 22, 23, 23, 25, 25, 25, 25, 25, 6] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 69 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 435) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/435: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCCN4Cc3ccccc3)c2c1) `ZINC001184489739.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184489739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489739 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCCN4Cc3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 15, 21, 23, 23, 23, 22, 23, 23, 23, 23, 23, 23, 23, 24, 26, 26, 26, 26, 26, 4, 4, 6, 6, 6, 4, 4, 4, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 24, 24, 26, 26, 26, 26, 26, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 65 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184489739 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739 Building ZINC001184489739 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184489739 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 432) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCCN4Cc3ccccc3)c2c1) `ZINC001184489739.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489739 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCCN4Cc3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 18, 21, 22, 22, 22, 21, 22, 22, 22, 22, 22, 22, 22, 23, 25, 25, 23, 25, 25, 6, 6, 7, 7, 7, 6, 6, 6, 22, 22, 22, 22, 21, 22, 22, 22, 22, 22, 22, 22, 22, 23, 23, 25, 25, 25, 25, 25, 6] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 69 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 433) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCCN4Cc3ccccc3)c2c1) `ZINC001184489739.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489739 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCCN4Cc3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 15, 21, 23, 23, 23, 22, 23, 23, 23, 23, 23, 23, 23, 24, 26, 26, 26, 26, 26, 4, 4, 6, 6, 6, 4, 4, 4, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 24, 24, 26, 26, 26, 26, 26, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 65 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 434) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/434: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCCN4Cc3ccccc3)c2c1) `ZINC001184489739.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184489739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489739 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCCN4Cc3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 18, 21, 22, 22, 22, 21, 22, 22, 22, 22, 22, 22, 22, 23, 25, 25, 23, 25, 25, 6, 6, 7, 7, 7, 6, 6, 6, 22, 22, 22, 22, 21, 22, 22, 22, 22, 22, 22, 22, 22, 23, 23, 25, 25, 25, 25, 25, 6] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 69 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 435) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/435: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCCN4Cc3ccccc3)c2c1) `ZINC001184489739.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184489739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489739 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCCN4Cc3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 15, 21, 23, 23, 23, 22, 23, 23, 23, 23, 23, 23, 23, 24, 26, 26, 26, 26, 26, 4, 4, 6, 6, 6, 4, 4, 4, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 24, 24, 26, 26, 26, 26, 26, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 65 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184489739 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739 Building ZINC001184489739 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184489739 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 432) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCCN4Cc3ccccc3)c2c1) `ZINC001184489739.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489739 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCCN4Cc3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 18, 21, 22, 22, 22, 21, 22, 22, 22, 22, 22, 22, 22, 23, 25, 25, 23, 25, 25, 6, 6, 7, 7, 7, 6, 6, 6, 22, 22, 22, 22, 21, 22, 22, 22, 22, 22, 22, 22, 22, 23, 23, 25, 25, 25, 25, 25, 6] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 69 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 433) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCCN4Cc3ccccc3)c2c1) `ZINC001184489739.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489739 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCCN4Cc3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 15, 21, 23, 23, 23, 22, 23, 23, 23, 23, 23, 23, 23, 24, 26, 26, 26, 26, 26, 4, 4, 6, 6, 6, 4, 4, 4, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 24, 24, 26, 26, 26, 26, 26, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 65 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 434) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/434: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCCN4Cc3ccccc3)c2c1) `ZINC001184489739.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184489739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489739 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCCN4Cc3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 18, 21, 22, 22, 22, 21, 22, 22, 22, 22, 22, 22, 22, 23, 25, 25, 23, 25, 25, 6, 6, 7, 7, 7, 6, 6, 6, 22, 22, 22, 22, 21, 22, 22, 22, 22, 22, 22, 22, 22, 23, 23, 25, 25, 25, 25, 25, 6] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 69 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 435) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/435: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCCN4Cc3ccccc3)c2c1) `ZINC001184489739.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184489739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489739 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCCN4Cc3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 15, 21, 23, 23, 23, 22, 23, 23, 23, 23, 23, 23, 23, 24, 26, 26, 26, 26, 26, 4, 4, 6, 6, 6, 4, 4, 4, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 24, 24, 26, 26, 26, 26, 26, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 65 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184489739 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489739 Building ZINC001184489743 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489743' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489743 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489743 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489743/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489743 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 436) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/436 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/436' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3C[C@H]4c5ccccc5N(S(C)(=O)=O)C[C@@H]4C3)c2c1) `ZINC001184489743.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489743/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489743 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3C[C@H]4c5ccccc5N(S(C)(=O)=O)C[C@@H]4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', '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, 7, 1, 1, 1, 1, 1, 1, 8, 14, 5, 11, 11, 5, 5, 7, 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, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 17, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 22, 22, 22, 18, 18, 18, 16, 5, 5, 7, 7, 7, 5, 5, 5, 18, 18, 18, 18, 18, 18, 22, 22, 22, 18, 18, 18, 18, 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: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489743 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489743/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489743 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 437) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/437 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/437' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3C[C@H]4c5ccccc5N(S(C)(=O)=O)C[C@@H]4C3)c2c1) `ZINC001184489743.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489743/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489743 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3C[C@H]4c5ccccc5N(S(C)(=O)=O)C[C@@H]4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', '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, 7, 1, 1, 1, 1, 1, 1, 8, 14, 5, 11, 11, 5, 5, 7, 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, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 18, 18, 18, 13, 13, 13, 11, 5, 5, 8, 8, 8, 5, 5, 5, 13, 13, 13, 13, 13, 13, 18, 18, 18, 13, 13, 13, 13, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489743 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184489743 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489743/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489743/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489743 Building ZINC001184489743 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489743' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489743 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489743 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489743/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489743 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 436) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3C[C@H]4c5ccccc5N(S(C)(=O)=O)C[C@@H]4C3)c2c1) `ZINC001184489743.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489743/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489743 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3C[C@H]4c5ccccc5N(S(C)(=O)=O)C[C@@H]4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', '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, 7, 1, 1, 1, 1, 1, 1, 8, 14, 5, 11, 11, 5, 5, 7, 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, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 17, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 22, 22, 22, 18, 18, 18, 16, 5, 5, 7, 7, 7, 5, 5, 5, 18, 18, 18, 18, 18, 18, 22, 22, 22, 18, 18, 18, 18, 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: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489743 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489743/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489743 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 437) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3C[C@H]4c5ccccc5N(S(C)(=O)=O)C[C@@H]4C3)c2c1) `ZINC001184489743.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489743/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489743 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3C[C@H]4c5ccccc5N(S(C)(=O)=O)C[C@@H]4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', '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, 7, 1, 1, 1, 1, 1, 1, 8, 14, 5, 11, 11, 5, 5, 7, 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, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 18, 18, 18, 13, 13, 13, 11, 5, 5, 8, 8, 8, 5, 5, 5, 13, 13, 13, 13, 13, 13, 18, 18, 18, 13, 13, 13, 13, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489743 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184489743 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489743/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489743/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489743 Building ZINC001184489747 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489747' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489747 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489747 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489747/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489747 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 438) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/438 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/438' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@@]4(CC(C(=O)NCc5ccncc5)=NO4)C3)c2c1) `ZINC001184489747.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489747 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@@]4(CC(C(=O)NCc5ccncc5)=NO4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 1, 11, 8, 5, 1, 1, 1, 8, 1, 1, 8, 12, 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] 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, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 29, 30, 30, 29, 30, 30, 4, 4, 4, 4, 4, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 29, 29, 30, 30, 30, 30, 4, 4, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489747 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489747/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489747 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 439) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/439 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/439' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@@]4(CC(C(=O)NCc5ccncc5)=NO4)C3)c2c1) `ZINC001184489747.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489747/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489747 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@@]4(CC(C(=O)NCc5ccncc5)=NO4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 1, 11, 8, 5, 1, 1, 1, 8, 1, 1, 8, 12, 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] 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, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 4, 6, 7, 7, 7, 7, 7, 7, 7, 17, 17, 17, 33, 34, 34, 33, 34, 34, 7, 7, 6, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 17, 33, 33, 34, 34, 34, 34, 7, 7, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489747 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184489747 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489747/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489747/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489747 Building ZINC001184489747 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489747' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489747 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489747 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489747/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489747 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 438) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@@]4(CC(C(=O)NCc5ccncc5)=NO4)C3)c2c1) `ZINC001184489747.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489747 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@@]4(CC(C(=O)NCc5ccncc5)=NO4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 1, 11, 8, 5, 1, 1, 1, 8, 1, 1, 8, 12, 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] 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, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 29, 30, 30, 29, 30, 30, 4, 4, 4, 4, 4, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 29, 29, 30, 30, 30, 30, 4, 4, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489747 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489747/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489747 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 439) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@@]4(CC(C(=O)NCc5ccncc5)=NO4)C3)c2c1) `ZINC001184489747.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489747/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489747 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@@]4(CC(C(=O)NCc5ccncc5)=NO4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 1, 11, 8, 5, 1, 1, 1, 8, 1, 1, 8, 12, 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] 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, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 4, 6, 7, 7, 7, 7, 7, 7, 7, 17, 17, 17, 33, 34, 34, 33, 34, 34, 7, 7, 6, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 17, 33, 33, 34, 34, 34, 34, 7, 7, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489747 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184489747 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489747/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489747/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489747 Building ZINC001184489748 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489748' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489748 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489748 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489748/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489748 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 440) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/440 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/440' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@]4(CC(C(=O)NCc5ccncc5)=NO4)C3)c2c1) `ZINC001184489748.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489748 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@]4(CC(C(=O)NCc5ccncc5)=NO4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 1, 11, 8, 5, 1, 1, 1, 8, 1, 1, 8, 12, 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] 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, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 4, 4, 6, 6, 6, 6, 6, 6, 6, 15, 15, 15, 31, 33, 33, 33, 33, 33, 6, 6, 5, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 15, 31, 31, 33, 33, 33, 33, 6, 6, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489748 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489748/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489748 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 441) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/441 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/441' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@]4(CC(C(=O)NCc5ccncc5)=NO4)C3)c2c1) `ZINC001184489748.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489748/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489748 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@]4(CC(C(=O)NCc5ccncc5)=NO4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 1, 11, 8, 5, 1, 1, 1, 8, 1, 1, 8, 12, 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] 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, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 30, 32, 32, 32, 32, 32, 3, 3, 3, 4, 4, 5, 5, 5, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 11, 30, 30, 32, 32, 32, 32, 3, 3, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489748 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184489748 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489748/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489748/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489748 Building ZINC001184489748 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489748' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489748 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489748 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489748/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489748 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 440) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@]4(CC(C(=O)NCc5ccncc5)=NO4)C3)c2c1) `ZINC001184489748.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489748 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@]4(CC(C(=O)NCc5ccncc5)=NO4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 1, 11, 8, 5, 1, 1, 1, 8, 1, 1, 8, 12, 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] 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, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 4, 4, 6, 6, 6, 6, 6, 6, 6, 15, 15, 15, 31, 33, 33, 33, 33, 33, 6, 6, 5, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 15, 31, 31, 33, 33, 33, 33, 6, 6, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489748 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489748/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489748 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 441) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@]4(CC(C(=O)NCc5ccncc5)=NO4)C3)c2c1) `ZINC001184489748.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489748/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489748 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@]4(CC(C(=O)NCc5ccncc5)=NO4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 1, 11, 8, 5, 1, 1, 1, 8, 1, 1, 8, 12, 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] 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, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 30, 32, 32, 32, 32, 32, 3, 3, 3, 4, 4, 5, 5, 5, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 11, 30, 30, 32, 32, 32, 32, 3, 3, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489748 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184489748 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489748/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489748/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489748 Building ZINC001184489771 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489771' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489771 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489771 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489771/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489771 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 442) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/442 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/442' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCCn4c(=O)cc(CNC(=O)CC(C)C)nc4C3)c2c1) `ZINC001184489771.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184489771 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCCn4c(=O)cc(CNC(=O)CC(C)C)nc4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 21, 21, 21, 36, 36, 36, 4, 4, 4, 4, 4, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 21, 36, 36, 36, 36, 36, 36, 36, 36, 36, 4, 4, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489771 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489771/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489771 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 443) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/443 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/443' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCCn4c(=O)cc(CNC(=O)CC(C)C)nc4C3)c2c1) `ZINC001184489771.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489771/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184489771 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCCn4c(=O)cc(CNC(=O)CC(C)C)nc4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 3, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 21, 21, 21, 38, 38, 38, 5, 5, 5, 3, 3, 4, 4, 4, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 14, 14, 21, 38, 38, 38, 38, 38, 38, 38, 38, 38, 5, 5, 3] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489771 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184489771 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489771/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489771/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489771 Building ZINC001184489771 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489771' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489771 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489771 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489771/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489771 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 442) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCCn4c(=O)cc(CNC(=O)CC(C)C)nc4C3)c2c1) `ZINC001184489771.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184489771 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCCn4c(=O)cc(CNC(=O)CC(C)C)nc4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 21, 21, 21, 36, 36, 36, 4, 4, 4, 4, 4, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 21, 36, 36, 36, 36, 36, 36, 36, 36, 36, 4, 4, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489771 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489771/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489771 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 443) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCCn4c(=O)cc(CNC(=O)CC(C)C)nc4C3)c2c1) `ZINC001184489771.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489771/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184489771 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCCn4c(=O)cc(CNC(=O)CC(C)C)nc4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 3, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 21, 21, 21, 38, 38, 38, 5, 5, 5, 3, 3, 4, 4, 4, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 14, 14, 21, 38, 38, 38, 38, 38, 38, 38, 38, 38, 5, 5, 3] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489771 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184489771 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489771/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489771/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489771 Building ZINC001184489904 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489904' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489904 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489904 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489904/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489904 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 444) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/444 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/444' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3c4ccccc4CN(C4CCNCC4)S3(=O)=O)c2c1) `ZINC001184489904.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489904 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3c4ccccc4CN(C4CCNCC4)S3(=O)=O)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 8, 5, 5, 5, 10, 5, 5, 14, 11, 11, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 5, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 22, 22, 22, 22, 22, 11, 11, 11, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 11, 11, 11, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489904 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489904/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489904 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 445) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/445 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/445' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3c4ccccc4CN(C4CCNCC4)S3(=O)=O)c2c1) `ZINC001184489904.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489904/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489904 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3c4ccccc4CN(C4CCNCC4)S3(=O)=O)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 8, 5, 5, 5, 10, 5, 5, 14, 11, 11, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 5, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 26, 26, 26, 26, 26, 15, 15, 15, 5, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15, 15, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489904 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184489904 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489904/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489904/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489904 Building ZINC001184489904 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489904' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489904 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489904 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489904/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489904 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 444) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3c4ccccc4CN(C4CCNCC4)S3(=O)=O)c2c1) `ZINC001184489904.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489904 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3c4ccccc4CN(C4CCNCC4)S3(=O)=O)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 8, 5, 5, 5, 10, 5, 5, 14, 11, 11, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 5, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 22, 22, 22, 22, 22, 11, 11, 11, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 11, 11, 11, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489904 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489904/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489904 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 445) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3c4ccccc4CN(C4CCNCC4)S3(=O)=O)c2c1) `ZINC001184489904.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489904/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489904 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3c4ccccc4CN(C4CCNCC4)S3(=O)=O)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 8, 5, 5, 5, 10, 5, 5, 14, 11, 11, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 5, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 26, 26, 26, 26, 26, 15, 15, 15, 5, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15, 15, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489904 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184489904 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489904/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489904/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489904 Building ZINC001184489977 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184489977 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 446) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/446 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/446' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCN4c3ccc(F)cc3)c2c1) `ZINC001184489977.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489977 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCN4c3ccc(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', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 17, 17, 11, 12, 17, 17, 8, 8, 9, 9, 9, 8, 8, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 17, 17, 17, 17, 8] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 447) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/447 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/447' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCN4c3ccc(F)cc3)c2c1) `ZINC001184489977.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489977 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCN4c3ccc(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', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 7, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 22, 22, 21, 21, 22, 22, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 22, 22, 22, 22, 6] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 53 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 448) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/448 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/448' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCN4c3ccc(F)cc3)c2c1) `ZINC001184489977.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184489977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489977 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCN4c3ccc(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', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 17, 17, 11, 12, 17, 17, 8, 8, 9, 9, 9, 8, 8, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 17, 17, 17, 17, 8] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 449) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/449 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/449' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCN4c3ccc(F)cc3)c2c1) `ZINC001184489977.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184489977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489977 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCN4c3ccc(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', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 7, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 22, 22, 21, 21, 22, 22, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 22, 22, 22, 22, 6] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 53 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184489977 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977 Building ZINC001184489977 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184489977 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 446) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCN4c3ccc(F)cc3)c2c1) `ZINC001184489977.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489977 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCN4c3ccc(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', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 17, 17, 11, 12, 17, 17, 8, 8, 9, 9, 9, 8, 8, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 17, 17, 17, 17, 8] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 447) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCN4c3ccc(F)cc3)c2c1) `ZINC001184489977.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489977 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCN4c3ccc(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', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 7, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 22, 22, 21, 21, 22, 22, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 22, 22, 22, 22, 6] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 53 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 448) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/448: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCN4c3ccc(F)cc3)c2c1) `ZINC001184489977.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184489977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489977 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCN4c3ccc(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', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 17, 17, 11, 12, 17, 17, 8, 8, 9, 9, 9, 8, 8, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 17, 17, 17, 17, 8] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 449) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/449: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCN4c3ccc(F)cc3)c2c1) `ZINC001184489977.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184489977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489977 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCN4c3ccc(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', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 7, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 22, 22, 21, 21, 22, 22, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 22, 22, 22, 22, 6] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 53 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184489977 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977 Building ZINC001184489977 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184489977 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 446) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCN4c3ccc(F)cc3)c2c1) `ZINC001184489977.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489977 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCN4c3ccc(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', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 17, 17, 11, 12, 17, 17, 8, 8, 9, 9, 9, 8, 8, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 17, 17, 17, 17, 8] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 447) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCN4c3ccc(F)cc3)c2c1) `ZINC001184489977.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489977 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCN4c3ccc(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', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 7, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 22, 22, 21, 21, 22, 22, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 22, 22, 22, 22, 6] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 53 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 448) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/448: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCN4c3ccc(F)cc3)c2c1) `ZINC001184489977.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184489977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489977 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCN4c3ccc(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', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 17, 17, 11, 12, 17, 17, 8, 8, 9, 9, 9, 8, 8, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 17, 17, 17, 17, 8] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 449) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/449: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCN4c3ccc(F)cc3)c2c1) `ZINC001184489977.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184489977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489977 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCN4c3ccc(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', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 7, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 22, 22, 21, 21, 22, 22, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 22, 22, 22, 22, 6] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 53 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184489977 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977 Building ZINC001184489977 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184489977 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 446) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCN4c3ccc(F)cc3)c2c1) `ZINC001184489977.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489977 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCN4c3ccc(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', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 17, 17, 11, 12, 17, 17, 8, 8, 9, 9, 9, 8, 8, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 17, 17, 17, 17, 8] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 447) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCN4c3ccc(F)cc3)c2c1) `ZINC001184489977.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489977 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCN4c3ccc(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', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 7, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 22, 22, 21, 21, 22, 22, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 22, 22, 22, 22, 6] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 53 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 448) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/448: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCN4c3ccc(F)cc3)c2c1) `ZINC001184489977.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184489977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489977 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCN4c3ccc(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', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 17, 17, 11, 12, 17, 17, 8, 8, 9, 9, 9, 8, 8, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 17, 17, 17, 17, 8] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 449) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/449: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCN4c3ccc(F)cc3)c2c1) `ZINC001184489977.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184489977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489977 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CC3)C(=O)NCN4c3ccc(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', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 7, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 22, 22, 21, 21, 22, 22, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 22, 22, 22, 22, 6] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 53 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184489977 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184489977 Building ZINC001184490039 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490039' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490039 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490039 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490039/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490039 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 450) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/450 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/450' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@@H]4CN(C(=O)c5ccco5)CCO[C@@H]4C3)c2c1) `ZINC001184490039.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490039 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@@H]4CN(C(=O)c5ccco5)CCO[C@@H]4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 12, 5, 7, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need 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, 5, 8, 13, 13, 13, 13, 13, 13, 13, 22, 22, 24, 24, 24, 24, 13, 13, 13, 13, 13, 13, 5, 5, 6, 6, 6, 5, 5, 5, 13, 13, 13, 13, 13, 13, 24, 24, 24, 13, 13, 13, 13, 13, 13, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490039 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490039/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490039 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 451) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/451 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/451' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@@H]4CN(C(=O)c5ccco5)CCO[C@@H]4C3)c2c1) `ZINC001184490039.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490039/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490039 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@@H]4CN(C(=O)c5ccco5)CCO[C@@H]4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 12, 5, 7, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 7, 14, 14, 14, 14, 14, 14, 14, 26, 26, 33, 33, 33, 33, 14, 14, 14, 14, 14, 14, 4, 4, 5, 5, 5, 4, 4, 4, 14, 14, 14, 14, 14, 14, 33, 33, 33, 14, 14, 14, 14, 14, 14, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490039 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490039 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490039/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490039/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490039 Building ZINC001184490039 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490039' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490039 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490039 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490039/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490039 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 450) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@@H]4CN(C(=O)c5ccco5)CCO[C@@H]4C3)c2c1) `ZINC001184490039.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490039 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@@H]4CN(C(=O)c5ccco5)CCO[C@@H]4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 12, 5, 7, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need 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, 5, 8, 13, 13, 13, 13, 13, 13, 13, 22, 22, 24, 24, 24, 24, 13, 13, 13, 13, 13, 13, 5, 5, 6, 6, 6, 5, 5, 5, 13, 13, 13, 13, 13, 13, 24, 24, 24, 13, 13, 13, 13, 13, 13, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490039 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490039/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490039 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 451) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@@H]4CN(C(=O)c5ccco5)CCO[C@@H]4C3)c2c1) `ZINC001184490039.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490039/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490039 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@@H]4CN(C(=O)c5ccco5)CCO[C@@H]4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 12, 5, 7, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 7, 14, 14, 14, 14, 14, 14, 14, 26, 26, 33, 33, 33, 33, 14, 14, 14, 14, 14, 14, 4, 4, 5, 5, 5, 4, 4, 4, 14, 14, 14, 14, 14, 14, 33, 33, 33, 14, 14, 14, 14, 14, 14, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490039 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490039 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490039/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490039/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490039 Building ZINC001184490049 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490049' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490049 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490049 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490049/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490049 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 452) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/452 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/452' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCO[C@H]4[C@H](OCCCn5cccn5)CC[C@@H]43)c2c1) `ZINC001184490049.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184490049 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCO[C@H]4[C@H](OCCCn5cccn5)CC[C@@H]43)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 7, 12, 5, 5, 5, 8, 1, 1, 1, 8, 5, 5, 5, 7, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 8, 16, 25, 33, 33, 33, 33, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 8, 8, 16, 16, 25, 25, 33, 33, 33, 2, 2, 2, 2, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 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/418326/xbt-8058088.46/working/building/ZINC001184490049 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490049/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490049 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 453) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/453 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/453' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCO[C@H]4[C@H](OCCCn5cccn5)CC[C@@H]43)c2c1) `ZINC001184490049.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490049/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184490049 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCO[C@H]4[C@H](OCCCn5cccn5)CC[C@@H]43)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 7, 12, 5, 5, 5, 8, 1, 1, 1, 8, 5, 5, 5, 7, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 8, 15, 24, 33, 40, 40, 40, 40, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 15, 15, 24, 24, 33, 33, 40, 40, 40, 2, 2, 2, 2, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490049 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490049 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490049/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490049/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490049 Building ZINC001184490049 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490049' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490049 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490049 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490049/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490049 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 452) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCO[C@H]4[C@H](OCCCn5cccn5)CC[C@@H]43)c2c1) `ZINC001184490049.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184490049 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCO[C@H]4[C@H](OCCCn5cccn5)CC[C@@H]43)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 7, 12, 5, 5, 5, 8, 1, 1, 1, 8, 5, 5, 5, 7, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 8, 16, 25, 33, 33, 33, 33, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 8, 8, 16, 16, 25, 25, 33, 33, 33, 2, 2, 2, 2, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 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/418326/xbt-8058088.46/working/building/ZINC001184490049 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490049/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490049 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 453) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCO[C@H]4[C@H](OCCCn5cccn5)CC[C@@H]43)c2c1) `ZINC001184490049.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490049/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184490049 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCO[C@H]4[C@H](OCCCn5cccn5)CC[C@@H]43)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 7, 12, 5, 5, 5, 8, 1, 1, 1, 8, 5, 5, 5, 7, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 8, 15, 24, 33, 40, 40, 40, 40, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 15, 15, 24, 24, 33, 33, 40, 40, 40, 2, 2, 2, 2, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490049 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490049 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490049/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490049/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490049 Building ZINC001184490069 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184490069 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 454) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/454 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/454' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CCC[C@H](C[N@]3CC[N@](C)CC3)O4)c2c1) `ZINC001184490069.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184490069 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CCC[C@H](C[N@]3CC[N@](C)CC3)O4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 10, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 24, 34, 34, 34, 34, 34, 34, 11, 3, 3, 4, 4, 4, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 24, 24, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 3] 50 rigid atoms, others: [9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 455) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/455 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/455' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CCC[C@H](C[N@]3CC[N@@](C)CC3)O4)c2c1) `ZINC001184490069.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184490069 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CCC[C@H](C[N@]3CC[N@@](C)CC3)O4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 10, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 23, 34, 34, 34, 34, 34, 34, 12, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 23, 23, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 3] 50 rigid atoms, others: [9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 456) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/456 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/456' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CCC[C@H](C[N@]3CC[N@](C)CC3)O4)c2c1) `ZINC001184490069.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184490069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184490069 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CCC[C@H](C[N@]3CC[N@](C)CC3)O4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 10, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 23, 32, 32, 32, 32, 32, 31, 11, 3, 3, 4, 4, 4, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 23, 23, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 31, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 457) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/457 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/457' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CCC[C@H](C[N@]3CC[N@@](C)CC3)O4)c2c1) `ZINC001184490069.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184490069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184490069 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CCC[C@H](C[N@]3CC[N@@](C)CC3)O4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 10, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 23, 31, 31, 31, 31, 31, 30, 10, 3, 3, 4, 4, 4, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 23, 23, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 30, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490069 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069 Building ZINC001184490069 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184490069 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 454) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CCC[C@H](C[N@]3CC[N@](C)CC3)O4)c2c1) `ZINC001184490069.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184490069 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CCC[C@H](C[N@]3CC[N@](C)CC3)O4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 10, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 24, 34, 34, 34, 34, 34, 34, 11, 3, 3, 4, 4, 4, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 24, 24, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 3] 50 rigid atoms, others: [9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 455) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CCC[C@H](C[N@]3CC[N@@](C)CC3)O4)c2c1) `ZINC001184490069.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184490069 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CCC[C@H](C[N@]3CC[N@@](C)CC3)O4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 10, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 23, 34, 34, 34, 34, 34, 34, 12, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 23, 23, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 3] 50 rigid atoms, others: [9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 456) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/456: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CCC[C@H](C[N@]3CC[N@](C)CC3)O4)c2c1) `ZINC001184490069.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184490069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184490069 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CCC[C@H](C[N@]3CC[N@](C)CC3)O4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 10, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 23, 32, 32, 32, 32, 32, 31, 11, 3, 3, 4, 4, 4, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 23, 23, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 31, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 457) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/457: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CCC[C@H](C[N@]3CC[N@@](C)CC3)O4)c2c1) `ZINC001184490069.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184490069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184490069 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CCC[C@H](C[N@]3CC[N@@](C)CC3)O4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 10, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 23, 31, 31, 31, 31, 31, 30, 10, 3, 3, 4, 4, 4, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 23, 23, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 30, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490069 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069 Building ZINC001184490069 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184490069 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 454) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CCC[C@H](C[N@]3CC[N@](C)CC3)O4)c2c1) `ZINC001184490069.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184490069 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CCC[C@H](C[N@]3CC[N@](C)CC3)O4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 10, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 24, 34, 34, 34, 34, 34, 34, 11, 3, 3, 4, 4, 4, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 24, 24, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 3] 50 rigid atoms, others: [9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 455) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CCC[C@H](C[N@]3CC[N@@](C)CC3)O4)c2c1) `ZINC001184490069.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184490069 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CCC[C@H](C[N@]3CC[N@@](C)CC3)O4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 10, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 23, 34, 34, 34, 34, 34, 34, 12, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 23, 23, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 3] 50 rigid atoms, others: [9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 456) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/456: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CCC[C@H](C[N@]3CC[N@](C)CC3)O4)c2c1) `ZINC001184490069.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184490069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184490069 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CCC[C@H](C[N@]3CC[N@](C)CC3)O4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 10, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 23, 32, 32, 32, 32, 32, 31, 11, 3, 3, 4, 4, 4, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 23, 23, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 31, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 457) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/457: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CCC[C@H](C[N@]3CC[N@@](C)CC3)O4)c2c1) `ZINC001184490069.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184490069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184490069 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CCC[C@H](C[N@]3CC[N@@](C)CC3)O4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 10, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 23, 31, 31, 31, 31, 31, 30, 10, 3, 3, 4, 4, 4, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 23, 23, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 30, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490069 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069 Building ZINC001184490069 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184490069 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 454) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CCC[C@H](C[N@]3CC[N@](C)CC3)O4)c2c1) `ZINC001184490069.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184490069 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CCC[C@H](C[N@]3CC[N@](C)CC3)O4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 10, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 24, 34, 34, 34, 34, 34, 34, 11, 3, 3, 4, 4, 4, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 24, 24, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 3] 50 rigid atoms, others: [9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 455) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CCC[C@H](C[N@]3CC[N@@](C)CC3)O4)c2c1) `ZINC001184490069.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184490069 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CCC[C@H](C[N@]3CC[N@@](C)CC3)O4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 10, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 23, 34, 34, 34, 34, 34, 34, 12, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 23, 23, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 3] 50 rigid atoms, others: [9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 456) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/456: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CCC[C@H](C[N@]3CC[N@](C)CC3)O4)c2c1) `ZINC001184490069.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184490069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184490069 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CCC[C@H](C[N@]3CC[N@](C)CC3)O4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 10, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 23, 32, 32, 32, 32, 32, 31, 11, 3, 3, 4, 4, 4, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 23, 23, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 31, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 457) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/457: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CCC[C@H](C[N@]3CC[N@@](C)CC3)O4)c2c1) `ZINC001184490069.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184490069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184490069 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CCC[C@H](C[N@]3CC[N@@](C)CC3)O4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 10, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 23, 31, 31, 31, 31, 31, 30, 10, 3, 3, 4, 4, 4, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 23, 23, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 30, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490069 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490069 Building ZINC001184490204 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184490204 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 458) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/458 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/458' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1) `ZINC001184490204.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184490204 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 1, 11, 5, 10, 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] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 14, 14, 14, 14, 14, 14, 14, 32, 32, 32, 32, 32, 32, 14, 14, 14, 14, 14, 4, 4, 5, 5, 5, 4, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14, 32, 32, 32, 32, 14, 14, 14, 14, 14, 4] 50 rigid atoms, others: [9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 459) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/459 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/459' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1) `ZINC001184490204.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184490204 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 1, 11, 5, 10, 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] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 14, 14, 14, 14, 14, 14, 14, 32, 32, 32, 32, 32, 32, 14, 14, 14, 14, 14, 4, 4, 5, 5, 5, 4, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14, 32, 32, 32, 32, 14, 14, 14, 14, 14, 4] 50 rigid atoms, others: [9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 460) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/460 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/460' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1) `ZINC001184490204.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184490204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184490204 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 1, 11, 5, 10, 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] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 1, 5, 14, 14, 14, 13, 14, 14, 14, 28, 28, 28, 28, 28, 28, 14, 14, 14, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14, 28, 28, 28, 28, 14, 14, 14, 14, 14, 4] 50 rigid atoms, others: [9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 461) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/461 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/461' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1) `ZINC001184490204.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184490204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184490204 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 1, 11, 5, 10, 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] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 1, 5, 14, 14, 14, 13, 14, 14, 14, 28, 28, 28, 28, 28, 28, 14, 14, 14, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14, 28, 28, 28, 28, 14, 14, 14, 14, 14, 4] 50 rigid atoms, others: [9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490204 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204 Building ZINC001184490204 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184490204 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 458) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1) `ZINC001184490204.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184490204 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 1, 11, 5, 10, 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] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 14, 14, 14, 14, 14, 14, 14, 32, 32, 32, 32, 32, 32, 14, 14, 14, 14, 14, 4, 4, 5, 5, 5, 4, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14, 32, 32, 32, 32, 14, 14, 14, 14, 14, 4] 50 rigid atoms, others: [9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 459) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1) `ZINC001184490204.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184490204 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 1, 11, 5, 10, 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] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 14, 14, 14, 14, 14, 14, 14, 32, 32, 32, 32, 32, 32, 14, 14, 14, 14, 14, 4, 4, 5, 5, 5, 4, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14, 32, 32, 32, 32, 14, 14, 14, 14, 14, 4] 50 rigid atoms, others: [9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 460) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/460: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1) `ZINC001184490204.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184490204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184490204 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 1, 11, 5, 10, 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] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 1, 5, 14, 14, 14, 13, 14, 14, 14, 28, 28, 28, 28, 28, 28, 14, 14, 14, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14, 28, 28, 28, 28, 14, 14, 14, 14, 14, 4] 50 rigid atoms, others: [9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 461) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/461: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1) `ZINC001184490204.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184490204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184490204 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 1, 11, 5, 10, 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] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 1, 5, 14, 14, 14, 13, 14, 14, 14, 28, 28, 28, 28, 28, 28, 14, 14, 14, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14, 28, 28, 28, 28, 14, 14, 14, 14, 14, 4] 50 rigid atoms, others: [9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490204 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204 Building ZINC001184490204 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184490204 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 458) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1) `ZINC001184490204.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184490204 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 1, 11, 5, 10, 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] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 14, 14, 14, 14, 14, 14, 14, 32, 32, 32, 32, 32, 32, 14, 14, 14, 14, 14, 4, 4, 5, 5, 5, 4, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14, 32, 32, 32, 32, 14, 14, 14, 14, 14, 4] 50 rigid atoms, others: [9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 459) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1) `ZINC001184490204.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184490204 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 1, 11, 5, 10, 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] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 14, 14, 14, 14, 14, 14, 14, 32, 32, 32, 32, 32, 32, 14, 14, 14, 14, 14, 4, 4, 5, 5, 5, 4, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14, 32, 32, 32, 32, 14, 14, 14, 14, 14, 4] 50 rigid atoms, others: [9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 460) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/460: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1) `ZINC001184490204.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184490204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184490204 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 1, 11, 5, 10, 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] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 1, 5, 14, 14, 14, 13, 14, 14, 14, 28, 28, 28, 28, 28, 28, 14, 14, 14, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14, 28, 28, 28, 28, 14, 14, 14, 14, 14, 4] 50 rigid atoms, others: [9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 461) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/461: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1) `ZINC001184490204.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184490204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184490204 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 1, 11, 5, 10, 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] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 1, 5, 14, 14, 14, 13, 14, 14, 14, 28, 28, 28, 28, 28, 28, 14, 14, 14, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14, 28, 28, 28, 28, 14, 14, 14, 14, 14, 4] 50 rigid atoms, others: [9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490204 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204 Building ZINC001184490204 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184490204 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 458) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1) `ZINC001184490204.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184490204 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 1, 11, 5, 10, 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] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 14, 14, 14, 14, 14, 14, 14, 32, 32, 32, 32, 32, 32, 14, 14, 14, 14, 14, 4, 4, 5, 5, 5, 4, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14, 32, 32, 32, 32, 14, 14, 14, 14, 14, 4] 50 rigid atoms, others: [9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 459) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1) `ZINC001184490204.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184490204 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 1, 11, 5, 10, 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] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 14, 14, 14, 14, 14, 14, 14, 32, 32, 32, 32, 32, 32, 14, 14, 14, 14, 14, 4, 4, 5, 5, 5, 4, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14, 32, 32, 32, 32, 14, 14, 14, 14, 14, 4] 50 rigid atoms, others: [9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 460) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/460: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1) `ZINC001184490204.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184490204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184490204 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 1, 11, 5, 10, 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] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 1, 5, 14, 14, 14, 13, 14, 14, 14, 28, 28, 28, 28, 28, 28, 14, 14, 14, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14, 28, 28, 28, 28, 14, 14, 14, 14, 14, 4] 50 rigid atoms, others: [9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 461) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/461: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1) `ZINC001184490204.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184490204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184490204 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 1, 11, 5, 10, 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] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 1, 5, 14, 14, 14, 13, 14, 14, 14, 28, 28, 28, 28, 28, 28, 14, 14, 14, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14, 28, 28, 28, 28, 14, 14, 14, 14, 14, 4] 50 rigid atoms, others: [9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490204 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490204 Building ZINC001184490205 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184490205 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 462) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/462 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/462' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1) `ZINC001184490205.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184490205 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 1, 11, 5, 10, 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] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 3, 12, 14, 14, 13, 14, 14, 14, 29, 29, 29, 29, 29, 29, 14, 14, 14, 14, 14, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 29, 29, 29, 29, 14, 14, 14, 14, 14, 3] 50 rigid atoms, others: [9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 463) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/463 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/463' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1) `ZINC001184490205.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184490205 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 1, 11, 5, 10, 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] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 3, 12, 14, 14, 13, 14, 14, 14, 29, 29, 29, 29, 29, 29, 14, 14, 14, 14, 14, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 29, 29, 29, 29, 14, 14, 14, 14, 14, 3] 50 rigid atoms, others: [9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 464) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/464 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/464' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1) `ZINC001184490205.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184490205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184490205 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 1, 11, 5, 10, 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] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 5, 14, 15, 15, 14, 15, 15, 15, 35, 35, 35, 35, 35, 35, 15, 15, 15, 15, 15, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15, 15, 35, 35, 35, 35, 15, 15, 15, 15, 15, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 465) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/465 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/465' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1) `ZINC001184490205.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184490205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184490205 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 1, 11, 5, 10, 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] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 5, 14, 15, 15, 14, 15, 15, 15, 35, 35, 35, 35, 35, 35, 15, 15, 15, 15, 15, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15, 15, 35, 35, 35, 35, 15, 15, 15, 15, 15, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490205 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205 Building ZINC001184490205 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184490205 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 462) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1) `ZINC001184490205.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184490205 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 1, 11, 5, 10, 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] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 3, 12, 14, 14, 13, 14, 14, 14, 29, 29, 29, 29, 29, 29, 14, 14, 14, 14, 14, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 29, 29, 29, 29, 14, 14, 14, 14, 14, 3] 50 rigid atoms, others: [9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 463) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1) `ZINC001184490205.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184490205 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 1, 11, 5, 10, 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] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 3, 12, 14, 14, 13, 14, 14, 14, 29, 29, 29, 29, 29, 29, 14, 14, 14, 14, 14, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 29, 29, 29, 29, 14, 14, 14, 14, 14, 3] 50 rigid atoms, others: [9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 464) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/464: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1) `ZINC001184490205.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184490205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184490205 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 1, 11, 5, 10, 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] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 5, 14, 15, 15, 14, 15, 15, 15, 35, 35, 35, 35, 35, 35, 15, 15, 15, 15, 15, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15, 15, 35, 35, 35, 35, 15, 15, 15, 15, 15, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 465) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/465: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1) `ZINC001184490205.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184490205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184490205 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 1, 11, 5, 10, 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] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 5, 14, 15, 15, 14, 15, 15, 15, 35, 35, 35, 35, 35, 35, 15, 15, 15, 15, 15, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15, 15, 35, 35, 35, 35, 15, 15, 15, 15, 15, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490205 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205 Building ZINC001184490205 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184490205 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 462) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1) `ZINC001184490205.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184490205 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 1, 11, 5, 10, 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] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 3, 12, 14, 14, 13, 14, 14, 14, 29, 29, 29, 29, 29, 29, 14, 14, 14, 14, 14, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 29, 29, 29, 29, 14, 14, 14, 14, 14, 3] 50 rigid atoms, others: [9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 463) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1) `ZINC001184490205.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184490205 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 1, 11, 5, 10, 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] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 3, 12, 14, 14, 13, 14, 14, 14, 29, 29, 29, 29, 29, 29, 14, 14, 14, 14, 14, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 29, 29, 29, 29, 14, 14, 14, 14, 14, 3] 50 rigid atoms, others: [9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 464) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/464: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1) `ZINC001184490205.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184490205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184490205 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 1, 11, 5, 10, 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] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 5, 14, 15, 15, 14, 15, 15, 15, 35, 35, 35, 35, 35, 35, 15, 15, 15, 15, 15, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15, 15, 35, 35, 35, 35, 15, 15, 15, 15, 15, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 465) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/465: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1) `ZINC001184490205.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184490205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184490205 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 1, 11, 5, 10, 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] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 5, 14, 15, 15, 14, 15, 15, 15, 35, 35, 35, 35, 35, 35, 15, 15, 15, 15, 15, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15, 15, 35, 35, 35, 35, 15, 15, 15, 15, 15, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490205 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205 Building ZINC001184490205 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184490205 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 462) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1) `ZINC001184490205.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184490205 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 1, 11, 5, 10, 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] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 3, 12, 14, 14, 13, 14, 14, 14, 29, 29, 29, 29, 29, 29, 14, 14, 14, 14, 14, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 29, 29, 29, 29, 14, 14, 14, 14, 14, 3] 50 rigid atoms, others: [9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 463) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1) `ZINC001184490205.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184490205 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 1, 11, 5, 10, 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] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 3, 12, 14, 14, 13, 14, 14, 14, 29, 29, 29, 29, 29, 29, 14, 14, 14, 14, 14, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 29, 29, 29, 29, 14, 14, 14, 14, 14, 3] 50 rigid atoms, others: [9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 464) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/464: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1) `ZINC001184490205.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184490205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184490205 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 1, 11, 5, 10, 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] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 5, 14, 15, 15, 14, 15, 15, 15, 35, 35, 35, 35, 35, 35, 15, 15, 15, 15, 15, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15, 15, 35, 35, 35, 35, 15, 15, 15, 15, 15, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 465) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/465: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1) `ZINC001184490205.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184490205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184490205 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@]4(C3)CN(c3cccc(F)c3)C(=O)CN4C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 1, 11, 5, 10, 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] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 5, 14, 15, 15, 14, 15, 15, 15, 35, 35, 35, 35, 35, 35, 15, 15, 15, 15, 15, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15, 15, 35, 35, 35, 35, 15, 15, 15, 15, 15, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490205 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490205 Building ZINC001184490225 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490225' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490225 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490225 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490225/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490225 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 466) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/466 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/466' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cnn2c1nccc2[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)CCO1) `ZINC001184490225.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490225/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001184490225 none CCOC(=O)c1cnn2c1nccc2[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 8, 1, 8, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 17, 17, 8, 17, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 4, 3, 2, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 7, 5, 5, 4, 4, 4, 24, 24, 24, 24, 24, 8, 8, 8, 4, 4, 5, 5, 5, 7, 7, 7, 5, 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, 56, 57]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490225 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490225/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490225 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 467) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/467 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/467' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cnn2c1nccc2[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)CCO1) `ZINC001184490225.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490225/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001184490225 none CCOC(=O)c1cnn2c1nccc2[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 8, 1, 8, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 20, 19, 10, 19, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 9, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 10, 10, 10, 6, 6, 6, 6, 6, 9, 9, 9, 6, 6, 6, 6, 6] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490225 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490225 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490225/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490225/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490225 Building ZINC001184490225 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490225' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490225 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490225 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490225/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490225 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 466) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCOC(=O)c1cnn2c1nccc2[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)CCO1) `ZINC001184490225.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490225/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001184490225 none CCOC(=O)c1cnn2c1nccc2[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 8, 1, 8, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 17, 17, 8, 17, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 4, 3, 2, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 7, 5, 5, 4, 4, 4, 24, 24, 24, 24, 24, 8, 8, 8, 4, 4, 5, 5, 5, 7, 7, 7, 5, 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, 56, 57]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490225 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490225/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490225 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 467) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCOC(=O)c1cnn2c1nccc2[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)CCO1) `ZINC001184490225.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490225/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001184490225 none CCOC(=O)c1cnn2c1nccc2[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 8, 1, 8, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 20, 19, 10, 19, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 9, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 10, 10, 10, 6, 6, 6, 6, 6, 9, 9, 9, 6, 6, 6, 6, 6] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490225 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490225 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490225/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490225/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490225 Building ZINC001184490226 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490226' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490226 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490226 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490226/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490226 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 468) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/468 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/468' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cnn2c1nccc2[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)CCO1) `ZINC001184490226.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001184490226 none CCOC(=O)c1cnn2c1nccc2[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 8, 1, 8, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 20, 19, 10, 19, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 9, 6, 6, 5, 5, 5, 28, 28, 28, 28, 28, 10, 10, 10, 5, 5, 6, 6, 6, 9, 9, 9, 6, 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: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490226 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490226/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490226 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 469) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/469 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/469' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cnn2c1nccc2[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)CCO1) `ZINC001184490226.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490226/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001184490226 none CCOC(=O)c1cnn2c1nccc2[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 8, 1, 8, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 19, 19, 9, 19, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 28, 28, 28, 28, 28, 9, 9, 9, 5, 5, 5, 5, 5, 7, 7, 7, 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: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490226 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490226 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490226/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490226/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490226 Building ZINC001184490226 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490226' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490226 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490226 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490226/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490226 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 468) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCOC(=O)c1cnn2c1nccc2[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)CCO1) `ZINC001184490226.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001184490226 none CCOC(=O)c1cnn2c1nccc2[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 8, 1, 8, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 20, 19, 10, 19, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 9, 6, 6, 5, 5, 5, 28, 28, 28, 28, 28, 10, 10, 10, 5, 5, 6, 6, 6, 9, 9, 9, 6, 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: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490226 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490226/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490226 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 469) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCOC(=O)c1cnn2c1nccc2[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)CCO1) `ZINC001184490226.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490226/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001184490226 none CCOC(=O)c1cnn2c1nccc2[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 8, 1, 8, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 19, 19, 9, 19, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 7, 5, 5, 5, 5, 5, 28, 28, 28, 28, 28, 9, 9, 9, 5, 5, 5, 5, 5, 7, 7, 7, 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: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490226 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490226 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490226/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490226/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490226 Building ZINC001184490244 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490244' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490244 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490244 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490244/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490244 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 470) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/470 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/470' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H]1CC2(CN1S(=O)(=O)C1CC1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2) `ZINC001184490244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184490244 none COC[C@@H]1CC2(CN1S(=O)(=O)C1CC1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 8, 14, 11, 11, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 23, 17, 17, 17, 17, 17, 17, 17, 17, 21, 21, 21, 26, 26, 17, 17, 5, 1, 9, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 5, 17, 17, 25, 25, 25, 23, 23, 17, 17, 17, 17, 26, 26, 26, 26, 26, 17, 17, 17, 17, 5, 5, 5, 8, 8, 8, 5, 17, 17, 17, 17] 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, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490244 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490244/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490244 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 471) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/471 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/471' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H]1CC2(CN1S(=O)(=O)C1CC1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2) `ZINC001184490244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184490244 none COC[C@@H]1CC2(CN1S(=O)(=O)C1CC1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 8, 14, 11, 11, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 22, 22, 22, 22, 22, 22, 22, 22, 24, 24, 24, 29, 29, 22, 22, 8, 1, 12, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 6, 6, 22, 22, 29, 29, 29, 27, 27, 22, 22, 22, 22, 29, 29, 29, 29, 29, 22, 22, 22, 22, 6, 6, 6, 8, 8, 8, 6, 22, 22, 22, 22] 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, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490244 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490244 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490244/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490244/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490244 Building ZINC001184490244 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490244' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490244 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490244 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490244/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490244 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 470) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/470: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H]1CC2(CN1S(=O)(=O)C1CC1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2) `ZINC001184490244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184490244 none COC[C@@H]1CC2(CN1S(=O)(=O)C1CC1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 8, 14, 11, 11, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 23, 17, 17, 17, 17, 17, 17, 17, 17, 21, 21, 21, 26, 26, 17, 17, 5, 1, 9, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 5, 17, 17, 25, 25, 25, 23, 23, 17, 17, 17, 17, 26, 26, 26, 26, 26, 17, 17, 17, 17, 5, 5, 5, 8, 8, 8, 5, 17, 17, 17, 17] 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, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490244 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490244/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490244 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 471) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/471: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H]1CC2(CN1S(=O)(=O)C1CC1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2) `ZINC001184490244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184490244 none COC[C@@H]1CC2(CN1S(=O)(=O)C1CC1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 8, 14, 11, 11, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 22, 22, 22, 22, 22, 22, 22, 22, 24, 24, 24, 29, 29, 22, 22, 8, 1, 12, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 6, 6, 22, 22, 29, 29, 29, 27, 27, 22, 22, 22, 22, 29, 29, 29, 29, 29, 22, 22, 22, 22, 6, 6, 6, 8, 8, 8, 6, 22, 22, 22, 22] 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, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490244 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490244 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490244/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490244/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490244 Building ZINC001184490247 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490247' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490247 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490247 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490247/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490247 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 472) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/472 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/472' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H]1CC2(CN1S(=O)(=O)C1CC1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2) `ZINC001184490247.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184490247 none COC[C@H]1CC2(CN1S(=O)(=O)C1CC1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 8, 14, 11, 11, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 23, 12, 12, 12, 12, 12, 12, 12, 12, 18, 18, 18, 21, 21, 12, 12, 7, 1, 9, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 6, 5, 5, 12, 12, 24, 24, 24, 23, 23, 12, 12, 12, 12, 21, 21, 21, 21, 21, 12, 12, 12, 12, 5, 5, 5, 6, 6, 6, 5, 12, 12, 12, 12] 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, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490247 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490247/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490247 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 473) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/473 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/473' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H]1CC2(CN1S(=O)(=O)C1CC1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2) `ZINC001184490247.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490247/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184490247 none COC[C@H]1CC2(CN1S(=O)(=O)C1CC1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 8, 14, 11, 11, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 11, 11, 11, 11, 16, 16, 16, 19, 19, 11, 11, 5, 1, 8, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 7, 6, 6, 11, 11, 21, 21, 21, 21, 21, 11, 11, 11, 11, 19, 19, 19, 19, 19, 11, 11, 11, 11, 6, 6, 6, 7, 7, 7, 6, 11, 11, 11, 11] 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, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490247 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490247 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490247/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490247/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490247 Building ZINC001184490247 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490247' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490247 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490247 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490247/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490247 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 472) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COC[C@H]1CC2(CN1S(=O)(=O)C1CC1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2) `ZINC001184490247.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184490247 none COC[C@H]1CC2(CN1S(=O)(=O)C1CC1)CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 8, 14, 11, 11, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 23, 12, 12, 12, 12, 12, 12, 12, 12, 18, 18, 18, 21, 21, 12, 12, 7, 1, 9, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 6, 5, 5, 12, 12, 24, 24, 24, 23, 23, 12, 12, 12, 12, 21, 21, 21, 21, 21, 12, 12, 12, 12, 5, 5, 5, 6, 6, 6, 5, 12, 12, 12, 12] 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, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490247 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490247/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490247 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 473) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COC[C@H]1CC2(CN1S(=O)(=O)C1CC1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2) `ZINC001184490247.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490247/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184490247 none COC[C@H]1CC2(CN1S(=O)(=O)C1CC1)CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(OC)cc31)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 5, 5, 8, 14, 11, 11, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 11, 11, 11, 11, 16, 16, 16, 19, 19, 11, 11, 5, 1, 8, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 7, 6, 6, 11, 11, 21, 21, 21, 21, 21, 11, 11, 11, 11, 19, 19, 19, 19, 19, 11, 11, 11, 11, 6, 6, 6, 7, 7, 7, 6, 11, 11, 11, 11] 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, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490247 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490247 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490247/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490247/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490247 Building ZINC001184490273 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490273' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490273 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490273 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490273/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490273 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 474) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/474 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/474' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(S(=O)(=O)NC2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(OC)cc43)CC2)cc1) `ZINC001184490273.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184490273 none COc1ccc(S(=O)(=O)NC2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(OC)cc43)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 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, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 30, 30, 27, 10, 27, 27, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 4, 4, 30, 30, 30, 30, 30, 30, 30, 10, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 4, 4, 4, 4, 4, 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, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490273 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490273/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490273 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 475) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/475 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/475' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(S(=O)(=O)NC2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(OC)cc43)CC2)cc1) `ZINC001184490273.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490273/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184490273 none COc1ccc(S(=O)(=O)NC2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(OC)cc43)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 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, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 31, 36, 36, 31, 9, 31, 31, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 4, 4, 36, 36, 36, 36, 36, 36, 36, 9, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 4, 4, 4, 4, 4, 36, 36] 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]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490273 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490273 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490273/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490273/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490273 Building ZINC001184490273 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490273' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490273 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490273 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490273/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490273 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 474) grep: /scratch/xiaobo/418326/xbt-8058088.46/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(S(=O)(=O)NC2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(OC)cc43)CC2)cc1) `ZINC001184490273.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184490273 none COc1ccc(S(=O)(=O)NC2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(OC)cc43)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 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, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 30, 30, 27, 10, 27, 27, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 4, 4, 30, 30, 30, 30, 30, 30, 30, 10, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 4, 4, 4, 4, 4, 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, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490273 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490273/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490273 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 475) grep: /scratch/xiaobo/418326/xbt-8058088.46/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(S(=O)(=O)NC2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(OC)cc43)CC2)cc1) `ZINC001184490273.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490273/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184490273 none COc1ccc(S(=O)(=O)NC2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(OC)cc43)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 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, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 31, 36, 36, 31, 9, 31, 31, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 4, 4, 36, 36, 36, 36, 36, 36, 36, 9, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 4, 4, 4, 4, 4, 36, 36] 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]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490273 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490273 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490273/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490273/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490273 Building ZINC001184490309 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490309' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490309 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490309 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490309/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490309 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 476) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/476 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/476' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4OCC[C@@H](C(=O)NCCc5ccncc5)[C@@H]4C3)c2c1) `ZINC001184490309.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001184490309 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4OCC[C@@H](C(=O)NCCc5ccncc5)[C@@H]4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 1, 1, 1, 8, 1, 1, 5, 7, 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, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 4, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 24, 31, 31, 31, 31, 31, 31, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 14, 24, 24, 31, 31, 31, 31, 31, 31, 6, 6, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490309 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490309/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490309 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 477) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/477 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/477' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4OCC[C@@H](C(=O)NCCc5ccncc5)[C@@H]4C3)c2c1) `ZINC001184490309.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490309/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001184490309 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4OCC[C@@H](C(=O)NCCc5ccncc5)[C@@H]4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 1, 1, 1, 8, 1, 1, 5, 7, 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, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 21, 30, 30, 30, 30, 30, 30, 4, 4, 4, 5, 5, 6, 6, 6, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 8, 21, 21, 30, 30, 30, 30, 30, 30, 4, 4, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490309 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490309 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490309/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490309/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490309 Building ZINC001184490309 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490309' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490309 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490309 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490309/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490309 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 476) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4OCC[C@@H](C(=O)NCCc5ccncc5)[C@@H]4C3)c2c1) `ZINC001184490309.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001184490309 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4OCC[C@@H](C(=O)NCCc5ccncc5)[C@@H]4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 1, 1, 1, 8, 1, 1, 5, 7, 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, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 4, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 24, 31, 31, 31, 31, 31, 31, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 14, 24, 24, 31, 31, 31, 31, 31, 31, 6, 6, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490309 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490309/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490309 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 477) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4OCC[C@@H](C(=O)NCCc5ccncc5)[C@@H]4C3)c2c1) `ZINC001184490309.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490309/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001184490309 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4OCC[C@@H](C(=O)NCCc5ccncc5)[C@@H]4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 1, 1, 1, 8, 1, 1, 5, 7, 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, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 21, 30, 30, 30, 30, 30, 30, 4, 4, 4, 5, 5, 6, 6, 6, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 8, 21, 21, 30, 30, 30, 30, 30, 30, 4, 4, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490309 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490309 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490309/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490309/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490309 Building ZINC001184490320 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184490320 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 478) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/478 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/478' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1) `ZINC001184490320.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490320 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 8, 1, 1, 15, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 11, 14, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 26, 26, 22, 25, 26, 26, 21, 5, 5, 6, 6, 6, 5, 5, 5, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 26, 26, 21, 21, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 479) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/479 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/479' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1) `ZINC001184490320.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490320 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 8, 1, 1, 15, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 10, 16, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 27, 27, 22, 24, 27, 27, 22, 5, 5, 8, 8, 8, 5, 5, 5, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 27, 27, 22, 22, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 480) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/480 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/480' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1) `ZINC001184490320.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184490320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490320 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 8, 1, 1, 15, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 11, 14, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 26, 26, 22, 25, 26, 26, 21, 5, 5, 6, 6, 6, 5, 5, 5, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 26, 26, 21, 21, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 481) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/481 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/481' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1) `ZINC001184490320.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184490320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490320 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 8, 1, 1, 15, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 10, 16, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 27, 27, 22, 24, 27, 27, 22, 5, 5, 8, 8, 8, 5, 5, 5, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 27, 27, 22, 22, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490320 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320 Building ZINC001184490320 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184490320 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 478) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1) `ZINC001184490320.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490320 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 8, 1, 1, 15, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 11, 14, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 26, 26, 22, 25, 26, 26, 21, 5, 5, 6, 6, 6, 5, 5, 5, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 26, 26, 21, 21, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 479) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1) `ZINC001184490320.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490320 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 8, 1, 1, 15, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 10, 16, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 27, 27, 22, 24, 27, 27, 22, 5, 5, 8, 8, 8, 5, 5, 5, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 27, 27, 22, 22, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 480) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/480: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1) `ZINC001184490320.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184490320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490320 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 8, 1, 1, 15, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 11, 14, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 26, 26, 22, 25, 26, 26, 21, 5, 5, 6, 6, 6, 5, 5, 5, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 26, 26, 21, 21, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 481) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/481: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1) `ZINC001184490320.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184490320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490320 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 8, 1, 1, 15, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 10, 16, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 27, 27, 22, 24, 27, 27, 22, 5, 5, 8, 8, 8, 5, 5, 5, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 27, 27, 22, 22, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490320 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320 Building ZINC001184490320 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184490320 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 478) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1) `ZINC001184490320.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490320 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 8, 1, 1, 15, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 11, 14, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 26, 26, 22, 25, 26, 26, 21, 5, 5, 6, 6, 6, 5, 5, 5, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 26, 26, 21, 21, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 479) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1) `ZINC001184490320.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490320 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 8, 1, 1, 15, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 10, 16, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 27, 27, 22, 24, 27, 27, 22, 5, 5, 8, 8, 8, 5, 5, 5, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 27, 27, 22, 22, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 480) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/480: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1) `ZINC001184490320.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184490320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490320 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 8, 1, 1, 15, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 11, 14, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 26, 26, 22, 25, 26, 26, 21, 5, 5, 6, 6, 6, 5, 5, 5, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 26, 26, 21, 21, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 481) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/481: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1) `ZINC001184490320.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184490320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490320 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 8, 1, 1, 15, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 10, 16, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 27, 27, 22, 24, 27, 27, 22, 5, 5, 8, 8, 8, 5, 5, 5, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 27, 27, 22, 22, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490320 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320 Building ZINC001184490320 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184490320 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 478) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1) `ZINC001184490320.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490320 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 8, 1, 1, 15, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 11, 14, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 26, 26, 22, 25, 26, 26, 21, 5, 5, 6, 6, 6, 5, 5, 5, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 26, 26, 21, 21, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 479) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1) `ZINC001184490320.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490320 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 8, 1, 1, 15, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 10, 16, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 27, 27, 22, 24, 27, 27, 22, 5, 5, 8, 8, 8, 5, 5, 5, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 27, 27, 22, 22, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 480) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/480: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1) `ZINC001184490320.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184490320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490320 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 8, 1, 1, 15, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 11, 14, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 26, 26, 22, 25, 26, 26, 21, 5, 5, 6, 6, 6, 5, 5, 5, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 26, 26, 21, 21, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 481) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/481: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1) `ZINC001184490320.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184490320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490320 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 8, 1, 1, 15, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 10, 16, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 27, 27, 22, 24, 27, 27, 22, 5, 5, 8, 8, 8, 5, 5, 5, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 27, 27, 22, 22, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490320 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490320 Building ZINC001184490321 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184490321 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 482) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/482 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/482' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1) `ZINC001184490321.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490321 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 8, 1, 1, 15, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 8, 10, 19, 19, 19, 19, 15, 19, 19, 19, 19, 19, 19, 22, 22, 19, 19, 22, 22, 19, 5, 5, 7, 7, 7, 5, 5, 5, 17, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 22, 22, 19, 19, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 483) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/483 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/483' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1) `ZINC001184490321.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490321 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 8, 1, 1, 15, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 7, 14, 22, 22, 22, 22, 20, 22, 22, 22, 22, 22, 22, 24, 24, 23, 23, 24, 24, 22, 5, 5, 6, 6, 6, 5, 5, 5, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 24, 24, 22, 22, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 62 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 484) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/484 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/484' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1) `ZINC001184490321.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184490321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490321 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 8, 1, 1, 15, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 8, 10, 19, 19, 19, 19, 15, 19, 19, 19, 19, 19, 19, 22, 22, 19, 19, 22, 22, 19, 5, 5, 7, 7, 7, 5, 5, 5, 17, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 22, 22, 19, 19, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 485) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/485 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/485' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1) `ZINC001184490321.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184490321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490321 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 8, 1, 1, 15, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 7, 14, 22, 22, 22, 22, 20, 22, 22, 22, 22, 22, 22, 24, 24, 23, 23, 24, 24, 22, 5, 5, 6, 6, 6, 5, 5, 5, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 24, 24, 22, 22, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 62 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490321 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321 Building ZINC001184490321 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184490321 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 482) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1) `ZINC001184490321.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490321 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 8, 1, 1, 15, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 8, 10, 19, 19, 19, 19, 15, 19, 19, 19, 19, 19, 19, 22, 22, 19, 19, 22, 22, 19, 5, 5, 7, 7, 7, 5, 5, 5, 17, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 22, 22, 19, 19, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 483) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1) `ZINC001184490321.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490321 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 8, 1, 1, 15, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 7, 14, 22, 22, 22, 22, 20, 22, 22, 22, 22, 22, 22, 24, 24, 23, 23, 24, 24, 22, 5, 5, 6, 6, 6, 5, 5, 5, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 24, 24, 22, 22, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 62 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 484) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/484: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1) `ZINC001184490321.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184490321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490321 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 8, 1, 1, 15, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 8, 10, 19, 19, 19, 19, 15, 19, 19, 19, 19, 19, 19, 22, 22, 19, 19, 22, 22, 19, 5, 5, 7, 7, 7, 5, 5, 5, 17, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 22, 22, 19, 19, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 485) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/485: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1) `ZINC001184490321.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184490321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490321 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 8, 1, 1, 15, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 7, 14, 22, 22, 22, 22, 20, 22, 22, 22, 22, 22, 22, 24, 24, 23, 23, 24, 24, 22, 5, 5, 6, 6, 6, 5, 5, 5, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 24, 24, 22, 22, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 62 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490321 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321 Building ZINC001184490321 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184490321 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 482) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1) `ZINC001184490321.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490321 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 8, 1, 1, 15, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 8, 10, 19, 19, 19, 19, 15, 19, 19, 19, 19, 19, 19, 22, 22, 19, 19, 22, 22, 19, 5, 5, 7, 7, 7, 5, 5, 5, 17, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 22, 22, 19, 19, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 483) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1) `ZINC001184490321.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490321 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 8, 1, 1, 15, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 7, 14, 22, 22, 22, 22, 20, 22, 22, 22, 22, 22, 22, 24, 24, 23, 23, 24, 24, 22, 5, 5, 6, 6, 6, 5, 5, 5, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 24, 24, 22, 22, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 62 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 484) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/484: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1) `ZINC001184490321.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184490321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490321 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 8, 1, 1, 15, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 8, 10, 19, 19, 19, 19, 15, 19, 19, 19, 19, 19, 19, 22, 22, 19, 19, 22, 22, 19, 5, 5, 7, 7, 7, 5, 5, 5, 17, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 22, 22, 19, 19, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 485) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/485: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1) `ZINC001184490321.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184490321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490321 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 8, 1, 1, 15, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 7, 14, 22, 22, 22, 22, 20, 22, 22, 22, 22, 22, 22, 24, 24, 23, 23, 24, 24, 22, 5, 5, 6, 6, 6, 5, 5, 5, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 24, 24, 22, 22, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 62 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490321 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321 Building ZINC001184490321 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184490321 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 482) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1) `ZINC001184490321.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490321 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 8, 1, 1, 15, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 8, 10, 19, 19, 19, 19, 15, 19, 19, 19, 19, 19, 19, 22, 22, 19, 19, 22, 22, 19, 5, 5, 7, 7, 7, 5, 5, 5, 17, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 22, 22, 19, 19, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 483) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1) `ZINC001184490321.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490321 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 8, 1, 1, 15, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 7, 14, 22, 22, 22, 22, 20, 22, 22, 22, 22, 22, 22, 24, 24, 23, 23, 24, 24, 22, 5, 5, 6, 6, 6, 5, 5, 5, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 24, 24, 22, 22, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 62 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 484) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/484: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1) `ZINC001184490321.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184490321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490321 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 8, 1, 1, 15, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 8, 10, 19, 19, 19, 19, 15, 19, 19, 19, 19, 19, 19, 22, 22, 19, 19, 22, 22, 19, 5, 5, 7, 7, 7, 5, 5, 5, 17, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 22, 22, 19, 19, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 485) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/485: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1) `ZINC001184490321.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184490321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490321 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@]4(C3)COCCN(c3ncc(F)cn3)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 8, 1, 1, 15, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 7, 14, 22, 22, 22, 22, 20, 22, 22, 22, 22, 22, 22, 24, 24, 23, 23, 24, 24, 22, 5, 5, 6, 6, 6, 5, 5, 5, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 24, 24, 22, 22, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 62 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490321 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490321 Building ZINC001184490337 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490337' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490337 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490337 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490337/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490337 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 486) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/486 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/486' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCOC[C@]4(CN(c5ccsc5)C(=O)CO4)C3)c2c1) `ZINC001184490337.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490337/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490337 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCOC[C@]4(CN(c5ccsc5)C(=O)CO4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 1, 1, 14, 1, 1, 11, 5, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 8, 10, 12, 12, 12, 12, 12, 12, 12, 12, 29, 29, 29, 29, 12, 12, 12, 12, 12, 5, 5, 6, 6, 6, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 29, 29, 29, 12, 12, 12, 12, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490337 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490337/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490337 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 487) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/487 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/487' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCOC[C@]4(CN(c5ccsc5)C(=O)CO4)C3)c2c1) `ZINC001184490337.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490337/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490337 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCOC[C@]4(CN(c5ccsc5)C(=O)CO4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 1, 1, 14, 1, 1, 11, 5, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 5, 7, 12, 12, 12, 12, 12, 12, 12, 12, 29, 29, 29, 29, 12, 12, 12, 12, 12, 4, 4, 6, 6, 6, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 29, 29, 29, 12, 12, 12, 12, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490337 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490337 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490337/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490337/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490337 Building ZINC001184490337 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490337' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490337 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490337 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490337/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490337 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 486) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCOC[C@]4(CN(c5ccsc5)C(=O)CO4)C3)c2c1) `ZINC001184490337.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490337/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490337 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCOC[C@]4(CN(c5ccsc5)C(=O)CO4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 1, 1, 14, 1, 1, 11, 5, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 8, 10, 12, 12, 12, 12, 12, 12, 12, 12, 29, 29, 29, 29, 12, 12, 12, 12, 12, 5, 5, 6, 6, 6, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 29, 29, 29, 12, 12, 12, 12, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490337 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490337/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490337 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 487) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCOC[C@]4(CN(c5ccsc5)C(=O)CO4)C3)c2c1) `ZINC001184490337.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490337/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490337 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCOC[C@]4(CN(c5ccsc5)C(=O)CO4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 1, 1, 14, 1, 1, 11, 5, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 5, 7, 12, 12, 12, 12, 12, 12, 12, 12, 29, 29, 29, 29, 12, 12, 12, 12, 12, 4, 4, 6, 6, 6, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 29, 29, 29, 12, 12, 12, 12, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490337 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490337 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490337/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490337/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490337 Building ZINC001184490338 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490338' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490338 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490338 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490338/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490338 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 488) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/488 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/488' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCOC[C@@]4(CN(c5ccsc5)C(=O)CO4)C3)c2c1) `ZINC001184490338.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490338 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCOC[C@@]4(CN(c5ccsc5)C(=O)CO4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 1, 1, 14, 1, 1, 11, 5, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 9, 9, 12, 12, 12, 12, 12, 12, 12, 12, 28, 28, 28, 28, 12, 12, 12, 12, 12, 4, 4, 7, 7, 7, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 28, 28, 28, 12, 12, 12, 12, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490338 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490338/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490338 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 489) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/489 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/489' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCOC[C@@]4(CN(c5ccsc5)C(=O)CO4)C3)c2c1) `ZINC001184490338.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490338/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490338 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCOC[C@@]4(CN(c5ccsc5)C(=O)CO4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 1, 1, 14, 1, 1, 11, 5, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 6, 6, 6, 6, 6, 5, 5, 8, 8, 8, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 6, 6, 6, 6, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490338 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490338 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490338/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490338/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490338 Building ZINC001184490338 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490338' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490338 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490338 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490338/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490338 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 488) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCOC[C@@]4(CN(c5ccsc5)C(=O)CO4)C3)c2c1) `ZINC001184490338.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490338 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCOC[C@@]4(CN(c5ccsc5)C(=O)CO4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 1, 1, 14, 1, 1, 11, 5, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 9, 9, 12, 12, 12, 12, 12, 12, 12, 12, 28, 28, 28, 28, 12, 12, 12, 12, 12, 4, 4, 7, 7, 7, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 28, 28, 28, 12, 12, 12, 12, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490338 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490338/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490338 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 489) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCOC[C@@]4(CN(c5ccsc5)C(=O)CO4)C3)c2c1) `ZINC001184490338.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490338/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490338 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCOC[C@@]4(CN(c5ccsc5)C(=O)CO4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 1, 1, 14, 1, 1, 11, 5, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 6, 6, 6, 6, 6, 5, 5, 8, 8, 8, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 6, 6, 6, 6, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490338 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490338 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490338/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490338/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490338 Building ZINC001184490417 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490417' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490417 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490417 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490417/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490417 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 490) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/490 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/490' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NCc3nnc4n3CCCN(C(=O)OC(C)(C)C)C4)c2c1) `ZINC001184490417.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490417/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490417 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NCc3nnc4n3CCCN(C(=O)OC(C)(C)C)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 8, 1, 8, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 12, 17, 17, 12, 17, 17, 17, 17, 17, 27, 27, 27, 27, 27, 27, 17, 5, 5, 5, 5, 5, 5, 5, 5, 3, 11, 11, 17, 17, 17, 17, 17, 17, 27, 27, 27, 27, 27, 27, 27, 27, 27, 17, 17, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490417 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490417/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490417 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 491) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/491 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/491' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NCc3nnc4n3CCCN(C(=O)OC(C)(C)C)C4)c2c1) `ZINC001184490417.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490417/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490417 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NCc3nnc4n3CCCN(C(=O)OC(C)(C)C)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 8, 1, 8, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 12, 17, 17, 12, 17, 17, 17, 17, 17, 27, 27, 27, 27, 27, 27, 17, 5, 5, 5, 5, 5, 5, 5, 5, 3, 11, 11, 17, 17, 17, 17, 17, 17, 27, 27, 27, 27, 27, 27, 27, 27, 27, 17, 17, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490417 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490417 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490417/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490417/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490417 Building ZINC001184490417 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490417' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490417 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490417 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490417/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490417 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 490) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NCc3nnc4n3CCCN(C(=O)OC(C)(C)C)C4)c2c1) `ZINC001184490417.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490417/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490417 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NCc3nnc4n3CCCN(C(=O)OC(C)(C)C)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 8, 1, 8, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 12, 17, 17, 12, 17, 17, 17, 17, 17, 27, 27, 27, 27, 27, 27, 17, 5, 5, 5, 5, 5, 5, 5, 5, 3, 11, 11, 17, 17, 17, 17, 17, 17, 27, 27, 27, 27, 27, 27, 27, 27, 27, 17, 17, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490417 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490417/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490417 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 491) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NCc3nnc4n3CCCN(C(=O)OC(C)(C)C)C4)c2c1) `ZINC001184490417.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490417/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490417 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NCc3nnc4n3CCCN(C(=O)OC(C)(C)C)C4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 8, 1, 8, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 12, 17, 17, 12, 17, 17, 17, 17, 17, 27, 27, 27, 27, 27, 27, 17, 5, 5, 5, 5, 5, 5, 5, 5, 3, 11, 11, 17, 17, 17, 17, 17, 17, 27, 27, 27, 27, 27, 27, 27, 27, 27, 17, 17, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490417 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490417 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490417/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490417/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490417 Building ZINC001184490445 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490445' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490445 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490445 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490445/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490445 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 492) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/492 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/492' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4CO[C@H](CNC(=O)c5ccncc5)[C@H]4C3)c2c1) `ZINC001184490445.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490445 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4CO[C@H](CNC(=O)c5ccncc5)[C@H]4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 5, 7, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 7, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 22, 34, 34, 34, 43, 43, 34, 43, 43, 12, 12, 12, 3, 3, 5, 5, 5, 3, 3, 3, 12, 12, 12, 12, 12, 12, 22, 22, 34, 43, 43, 43, 43, 12, 12, 3] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490445 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490445/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490445 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 493) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/493 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/493' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4CO[C@H](CNC(=O)c5ccncc5)[C@H]4C3)c2c1) `ZINC001184490445.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490445/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490445 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4CO[C@H](CNC(=O)c5ccncc5)[C@H]4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 5, 7, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 20, 32, 32, 32, 40, 40, 40, 40, 40, 7, 7, 7, 3, 3, 5, 5, 5, 3, 3, 3, 7, 7, 7, 7, 7, 7, 20, 20, 32, 40, 40, 40, 40, 7, 7, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490445 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490445 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490445/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490445/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490445 Building ZINC001184490445 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490445' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490445 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490445 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490445/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490445 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 492) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4CO[C@H](CNC(=O)c5ccncc5)[C@H]4C3)c2c1) `ZINC001184490445.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490445 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4CO[C@H](CNC(=O)c5ccncc5)[C@H]4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 5, 7, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 7, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 22, 34, 34, 34, 43, 43, 34, 43, 43, 12, 12, 12, 3, 3, 5, 5, 5, 3, 3, 3, 12, 12, 12, 12, 12, 12, 22, 22, 34, 43, 43, 43, 43, 12, 12, 3] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490445 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490445/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490445 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 493) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4CO[C@H](CNC(=O)c5ccncc5)[C@H]4C3)c2c1) `ZINC001184490445.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490445/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490445 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4CO[C@H](CNC(=O)c5ccncc5)[C@H]4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 5, 7, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 20, 32, 32, 32, 40, 40, 40, 40, 40, 7, 7, 7, 3, 3, 5, 5, 5, 3, 3, 3, 7, 7, 7, 7, 7, 7, 20, 20, 32, 40, 40, 40, 40, 7, 7, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490445 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490445 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490445/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490445/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490445 Building ZINC001184490467 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490467' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490467 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490467 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490467/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490467 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 494) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/494 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/494' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4C(=O)N(Cc5cccc(C)n5)CCO[C@H]4C3)c2c1) `ZINC001184490467.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490467/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184490467 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4C(=O)N(Cc5cccc(C)n5)CCO[C@H]4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 8, 5, 5, 12, 5, 7, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 9, 11, 11, 11, 11, 11, 11, 11, 11, 28, 30, 30, 30, 30, 30, 30, 11, 11, 11, 11, 11, 11, 4, 4, 5, 5, 5, 4, 4, 4, 11, 11, 11, 11, 28, 28, 30, 30, 30, 30, 30, 30, 11, 11, 11, 11, 11, 11, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490467 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490467/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490467 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 495) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/495 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/495' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4C(=O)N(Cc5cccc(C)n5)CCO[C@H]4C3)c2c1) `ZINC001184490467.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490467/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184490467 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4C(=O)N(Cc5cccc(C)n5)CCO[C@H]4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 8, 5, 5, 12, 5, 7, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 6, 8, 10, 10, 10, 10, 10, 10, 10, 10, 30, 30, 30, 30, 30, 30, 30, 10, 10, 10, 10, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 10, 30, 30, 30, 30, 30, 30, 30, 30, 10, 10, 10, 10, 10, 10, 3] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490467 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490467 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490467/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490467/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490467 Building ZINC001184490467 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490467' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490467 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490467 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490467/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490467 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 494) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4C(=O)N(Cc5cccc(C)n5)CCO[C@H]4C3)c2c1) `ZINC001184490467.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490467/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184490467 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4C(=O)N(Cc5cccc(C)n5)CCO[C@H]4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 8, 5, 5, 12, 5, 7, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 9, 11, 11, 11, 11, 11, 11, 11, 11, 28, 30, 30, 30, 30, 30, 30, 11, 11, 11, 11, 11, 11, 4, 4, 5, 5, 5, 4, 4, 4, 11, 11, 11, 11, 28, 28, 30, 30, 30, 30, 30, 30, 11, 11, 11, 11, 11, 11, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490467 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490467/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490467 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 495) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4C(=O)N(Cc5cccc(C)n5)CCO[C@H]4C3)c2c1) `ZINC001184490467.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490467/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184490467 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4C(=O)N(Cc5cccc(C)n5)CCO[C@H]4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 8, 5, 5, 12, 5, 7, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 6, 8, 10, 10, 10, 10, 10, 10, 10, 10, 30, 30, 30, 30, 30, 30, 30, 10, 10, 10, 10, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 10, 30, 30, 30, 30, 30, 30, 30, 30, 10, 10, 10, 10, 10, 10, 3] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490467 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490467 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490467/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490467/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490467 Building ZINC001184490469 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184490469 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 496) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/496 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/496' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NC[C@H]3C[C@H]4CN(C(=O)OC(C)(C)C)CCN4C3)c2c1) `ZINC001184490469.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184490469 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NC[C@H]3C[C@H]4CN(C(=O)OC(C)(C)C)CCN4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 17, 28, 28, 28, 28, 28, 28, 28, 32, 32, 32, 32, 32, 32, 28, 28, 28, 28, 4, 4, 4, 4, 4, 4, 4, 4, 3, 17, 17, 28, 28, 28, 28, 32, 32, 32, 32, 32, 32, 32, 32, 32, 28, 28, 28, 28, 28, 28, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 497) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/497 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/497' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NC[C@H]3C[C@H]4CN(C(=O)OC(C)(C)C)CCN4C3)c2c1) `ZINC001184490469.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184490469 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NC[C@H]3C[C@H]4CN(C(=O)OC(C)(C)C)CCN4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 17, 28, 28, 28, 28, 28, 28, 28, 32, 32, 32, 32, 32, 32, 28, 28, 28, 28, 4, 4, 4, 4, 4, 4, 4, 4, 3, 17, 17, 28, 28, 28, 28, 32, 32, 32, 32, 32, 32, 32, 32, 32, 28, 28, 28, 28, 28, 28, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 498) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/498 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/498' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NC[C@H]3C[C@H]4CN(C(=O)OC(C)(C)C)CCN4C3)c2c1) `ZINC001184490469.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184490469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184490469 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NC[C@H]3C[C@H]4CN(C(=O)OC(C)(C)C)CCN4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 16, 25, 25, 25, 25, 25, 25, 25, 29, 29, 29, 29, 29, 29, 25, 25, 25, 25, 4, 4, 4, 4, 4, 4, 4, 4, 3, 16, 16, 25, 25, 25, 25, 29, 29, 29, 29, 29, 29, 29, 29, 29, 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, 60, 61, 62, 63, 64]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 499) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/499 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/499' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NC[C@H]3C[C@H]4CN(C(=O)OC(C)(C)C)CCN4C3)c2c1) `ZINC001184490469.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184490469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184490469 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NC[C@H]3C[C@H]4CN(C(=O)OC(C)(C)C)CCN4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 16, 25, 25, 25, 25, 25, 25, 25, 29, 29, 29, 29, 29, 29, 25, 25, 25, 25, 4, 4, 4, 4, 4, 4, 4, 4, 3, 16, 16, 25, 25, 25, 25, 29, 29, 29, 29, 29, 29, 29, 29, 29, 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, 60, 61, 62, 63, 64]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490469 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469 Building ZINC001184490469 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184490469 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 496) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NC[C@H]3C[C@H]4CN(C(=O)OC(C)(C)C)CCN4C3)c2c1) `ZINC001184490469.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184490469 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NC[C@H]3C[C@H]4CN(C(=O)OC(C)(C)C)CCN4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 17, 28, 28, 28, 28, 28, 28, 28, 32, 32, 32, 32, 32, 32, 28, 28, 28, 28, 4, 4, 4, 4, 4, 4, 4, 4, 3, 17, 17, 28, 28, 28, 28, 32, 32, 32, 32, 32, 32, 32, 32, 32, 28, 28, 28, 28, 28, 28, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 497) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NC[C@H]3C[C@H]4CN(C(=O)OC(C)(C)C)CCN4C3)c2c1) `ZINC001184490469.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184490469 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NC[C@H]3C[C@H]4CN(C(=O)OC(C)(C)C)CCN4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 17, 28, 28, 28, 28, 28, 28, 28, 32, 32, 32, 32, 32, 32, 28, 28, 28, 28, 4, 4, 4, 4, 4, 4, 4, 4, 3, 17, 17, 28, 28, 28, 28, 32, 32, 32, 32, 32, 32, 32, 32, 32, 28, 28, 28, 28, 28, 28, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 498) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/498: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NC[C@H]3C[C@H]4CN(C(=O)OC(C)(C)C)CCN4C3)c2c1) `ZINC001184490469.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184490469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184490469 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NC[C@H]3C[C@H]4CN(C(=O)OC(C)(C)C)CCN4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 16, 25, 25, 25, 25, 25, 25, 25, 29, 29, 29, 29, 29, 29, 25, 25, 25, 25, 4, 4, 4, 4, 4, 4, 4, 4, 3, 16, 16, 25, 25, 25, 25, 29, 29, 29, 29, 29, 29, 29, 29, 29, 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, 60, 61, 62, 63, 64]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 499) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/499: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NC[C@H]3C[C@H]4CN(C(=O)OC(C)(C)C)CCN4C3)c2c1) `ZINC001184490469.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184490469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184490469 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NC[C@H]3C[C@H]4CN(C(=O)OC(C)(C)C)CCN4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 16, 25, 25, 25, 25, 25, 25, 25, 29, 29, 29, 29, 29, 29, 25, 25, 25, 25, 4, 4, 4, 4, 4, 4, 4, 4, 3, 16, 16, 25, 25, 25, 25, 29, 29, 29, 29, 29, 29, 29, 29, 29, 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, 60, 61, 62, 63, 64]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490469 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469 Building ZINC001184490469 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184490469 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 496) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NC[C@H]3C[C@H]4CN(C(=O)OC(C)(C)C)CCN4C3)c2c1) `ZINC001184490469.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184490469 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NC[C@H]3C[C@H]4CN(C(=O)OC(C)(C)C)CCN4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 17, 28, 28, 28, 28, 28, 28, 28, 32, 32, 32, 32, 32, 32, 28, 28, 28, 28, 4, 4, 4, 4, 4, 4, 4, 4, 3, 17, 17, 28, 28, 28, 28, 32, 32, 32, 32, 32, 32, 32, 32, 32, 28, 28, 28, 28, 28, 28, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 497) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NC[C@H]3C[C@H]4CN(C(=O)OC(C)(C)C)CCN4C3)c2c1) `ZINC001184490469.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184490469 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NC[C@H]3C[C@H]4CN(C(=O)OC(C)(C)C)CCN4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 17, 28, 28, 28, 28, 28, 28, 28, 32, 32, 32, 32, 32, 32, 28, 28, 28, 28, 4, 4, 4, 4, 4, 4, 4, 4, 3, 17, 17, 28, 28, 28, 28, 32, 32, 32, 32, 32, 32, 32, 32, 32, 28, 28, 28, 28, 28, 28, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 498) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/498: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NC[C@H]3C[C@H]4CN(C(=O)OC(C)(C)C)CCN4C3)c2c1) `ZINC001184490469.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184490469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184490469 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NC[C@H]3C[C@H]4CN(C(=O)OC(C)(C)C)CCN4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 16, 25, 25, 25, 25, 25, 25, 25, 29, 29, 29, 29, 29, 29, 25, 25, 25, 25, 4, 4, 4, 4, 4, 4, 4, 4, 3, 16, 16, 25, 25, 25, 25, 29, 29, 29, 29, 29, 29, 29, 29, 29, 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, 60, 61, 62, 63, 64]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 499) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/499: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NC[C@H]3C[C@H]4CN(C(=O)OC(C)(C)C)CCN4C3)c2c1) `ZINC001184490469.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184490469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184490469 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NC[C@H]3C[C@H]4CN(C(=O)OC(C)(C)C)CCN4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 16, 25, 25, 25, 25, 25, 25, 25, 29, 29, 29, 29, 29, 29, 25, 25, 25, 25, 4, 4, 4, 4, 4, 4, 4, 4, 3, 16, 16, 25, 25, 25, 25, 29, 29, 29, 29, 29, 29, 29, 29, 29, 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, 60, 61, 62, 63, 64]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490469 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469 Building ZINC001184490469 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184490469 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 496) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NC[C@H]3C[C@H]4CN(C(=O)OC(C)(C)C)CCN4C3)c2c1) `ZINC001184490469.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184490469 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NC[C@H]3C[C@H]4CN(C(=O)OC(C)(C)C)CCN4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 17, 28, 28, 28, 28, 28, 28, 28, 32, 32, 32, 32, 32, 32, 28, 28, 28, 28, 4, 4, 4, 4, 4, 4, 4, 4, 3, 17, 17, 28, 28, 28, 28, 32, 32, 32, 32, 32, 32, 32, 32, 32, 28, 28, 28, 28, 28, 28, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 497) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NC[C@H]3C[C@H]4CN(C(=O)OC(C)(C)C)CCN4C3)c2c1) `ZINC001184490469.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184490469 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NC[C@H]3C[C@H]4CN(C(=O)OC(C)(C)C)CCN4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 17, 28, 28, 28, 28, 28, 28, 28, 32, 32, 32, 32, 32, 32, 28, 28, 28, 28, 4, 4, 4, 4, 4, 4, 4, 4, 3, 17, 17, 28, 28, 28, 28, 32, 32, 32, 32, 32, 32, 32, 32, 32, 28, 28, 28, 28, 28, 28, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 498) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/498: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NC[C@H]3C[C@H]4CN(C(=O)OC(C)(C)C)CCN4C3)c2c1) `ZINC001184490469.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184490469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184490469 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NC[C@H]3C[C@H]4CN(C(=O)OC(C)(C)C)CCN4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 16, 25, 25, 25, 25, 25, 25, 25, 29, 29, 29, 29, 29, 29, 25, 25, 25, 25, 4, 4, 4, 4, 4, 4, 4, 4, 3, 16, 16, 25, 25, 25, 25, 29, 29, 29, 29, 29, 29, 29, 29, 29, 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, 60, 61, 62, 63, 64]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 499) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/499: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NC[C@H]3C[C@H]4CN(C(=O)OC(C)(C)C)CCN4C3)c2c1) `ZINC001184490469.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184490469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184490469 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NC[C@H]3C[C@H]4CN(C(=O)OC(C)(C)C)CCN4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 16, 25, 25, 25, 25, 25, 25, 25, 29, 29, 29, 29, 29, 29, 25, 25, 25, 25, 4, 4, 4, 4, 4, 4, 4, 4, 3, 16, 16, 25, 25, 25, 25, 29, 29, 29, 29, 29, 29, 29, 29, 29, 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, 60, 61, 62, 63, 64]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490469 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490469 Building ZINC001184490520 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490520' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490520 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490520 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490520/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490520 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 500) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/500 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/500' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4OC[C@@H](C(=O)N5CCCCO5)C[C@H]4C3)c2c1) `ZINC001184490520.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490520 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4OC[C@@H](C(=O)N5CCCCO5)C[C@H]4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 7, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 4, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 19, 21, 21, 21, 21, 21, 6, 6, 6, 6, 5, 5, 8, 8, 8, 5, 5, 5, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 53 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490520 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490520/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490520 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 501) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/501 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/501' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4OC[C@@H](C(=O)N5CCCCO5)C[C@H]4C3)c2c1) `ZINC001184490520.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490520/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490520 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4OC[C@@H](C(=O)N5CCCCO5)C[C@H]4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 7, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 22, 25, 25, 25, 25, 25, 5, 5, 5, 5, 5, 5, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 25, 25, 25, 25, 25, 25, 25, 25, 5, 5, 5, 5, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 60 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490520 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490520 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490520/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490520/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490520 Building ZINC001184490520 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490520' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490520 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490520 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490520/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490520 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 500) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4OC[C@@H](C(=O)N5CCCCO5)C[C@H]4C3)c2c1) `ZINC001184490520.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490520 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4OC[C@@H](C(=O)N5CCCCO5)C[C@H]4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 7, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 4, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 19, 21, 21, 21, 21, 21, 6, 6, 6, 6, 5, 5, 8, 8, 8, 5, 5, 5, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 53 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490520 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490520/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490520 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 501) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4OC[C@@H](C(=O)N5CCCCO5)C[C@H]4C3)c2c1) `ZINC001184490520.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490520/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490520 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4OC[C@@H](C(=O)N5CCCCO5)C[C@H]4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 7, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 22, 25, 25, 25, 25, 25, 5, 5, 5, 5, 5, 5, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 25, 25, 25, 25, 25, 25, 25, 25, 5, 5, 5, 5, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 60 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490520 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490520 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490520/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490520/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490520 Building ZINC001184490531 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490531' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490531 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490531 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490531/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490531 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 502) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/502 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/502' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3C[C@@H](NC(=O)c4cccnc4)[C@H]4OCCC[C@H]4C3)c2c1) `ZINC001184490531.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490531 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3C[C@@H](NC(=O)c4cccnc4)[C@H]4OCCC[C@H]4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 8, 1, 5, 7, 12, 5, 5, 5, 5, 7, 5, 1, 1, 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, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 4, 5, 6, 6, 6, 6, 16, 16, 16, 27, 27, 27, 27, 27, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 8, 8, 8, 5, 5, 5, 6, 6, 16, 27, 27, 27, 27, 6, 6, 6, 6, 6, 6, 6, 6, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490531 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490531/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490531 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 503) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/503 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/503' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3C[C@@H](NC(=O)c4cccnc4)[C@H]4OCCC[C@H]4C3)c2c1) `ZINC001184490531.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490531/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490531 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3C[C@@H](NC(=O)c4cccnc4)[C@H]4OCCC[C@H]4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 8, 1, 5, 7, 12, 5, 5, 5, 5, 7, 5, 1, 1, 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, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 8, 8, 8, 8, 16, 16, 16, 29, 29, 29, 29, 29, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 5, 5, 5, 4, 4, 4, 8, 8, 16, 29, 29, 29, 29, 8, 8, 8, 8, 8, 8, 8, 8, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490531 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490531 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490531/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490531/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490531 Building ZINC001184490531 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490531' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490531 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490531 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490531/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490531 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 502) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3C[C@@H](NC(=O)c4cccnc4)[C@H]4OCCC[C@H]4C3)c2c1) `ZINC001184490531.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490531 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3C[C@@H](NC(=O)c4cccnc4)[C@H]4OCCC[C@H]4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 8, 1, 5, 7, 12, 5, 5, 5, 5, 7, 5, 1, 1, 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, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 4, 5, 6, 6, 6, 6, 16, 16, 16, 27, 27, 27, 27, 27, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 8, 8, 8, 5, 5, 5, 6, 6, 16, 27, 27, 27, 27, 6, 6, 6, 6, 6, 6, 6, 6, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490531 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490531/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490531 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 503) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3C[C@@H](NC(=O)c4cccnc4)[C@H]4OCCC[C@H]4C3)c2c1) `ZINC001184490531.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490531/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490531 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3C[C@@H](NC(=O)c4cccnc4)[C@H]4OCCC[C@H]4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 8, 1, 5, 7, 12, 5, 5, 5, 5, 7, 5, 1, 1, 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, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 8, 8, 8, 8, 16, 16, 16, 29, 29, 29, 29, 29, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 5, 5, 5, 4, 4, 4, 8, 8, 16, 29, 29, 29, 29, 8, 8, 8, 8, 8, 8, 8, 8, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490531 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490531 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490531/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490531/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490531 Building ZINC001184490876 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490876' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490876 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490876 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490876/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490876 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 504) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/504 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/504' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3C[C@H](NC(=O)c4cscn4)[C@@H]4OCCC[C@@H]43)c2c1) `ZINC001184490876.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490876 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3C[C@H](NC(=O)c4cscn4)[C@@H]4OCCC[C@@H]43)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 14, 1, 8, 5, 7, 12, 5, 5, 5, 5, 7, 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, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 10, 10, 10, 10, 22, 22, 22, 29, 29, 29, 29, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 7, 7, 7, 4, 4, 4, 10, 10, 22, 29, 29, 10, 10, 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490876 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490876/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490876 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 505) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/505 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/505' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3C[C@H](NC(=O)c4cscn4)[C@@H]4OCCC[C@@H]43)c2c1) `ZINC001184490876.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490876/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490876 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3C[C@H](NC(=O)c4cscn4)[C@@H]4OCCC[C@@H]43)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 14, 1, 8, 5, 7, 12, 5, 5, 5, 5, 7, 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, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 6, 6, 9, 9, 9, 9, 19, 19, 19, 21, 21, 21, 21, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 8, 8, 8, 5, 5, 5, 9, 9, 19, 21, 21, 9, 9, 9, 9, 9, 9, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490876 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490876 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490876/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490876/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490876 Building ZINC001184490876 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490876' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490876 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490876 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490876/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490876 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 504) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3C[C@H](NC(=O)c4cscn4)[C@@H]4OCCC[C@@H]43)c2c1) `ZINC001184490876.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490876 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3C[C@H](NC(=O)c4cscn4)[C@@H]4OCCC[C@@H]43)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 14, 1, 8, 5, 7, 12, 5, 5, 5, 5, 7, 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, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 10, 10, 10, 10, 22, 22, 22, 29, 29, 29, 29, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 7, 7, 7, 4, 4, 4, 10, 10, 22, 29, 29, 10, 10, 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490876 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490876/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490876 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 505) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3C[C@H](NC(=O)c4cscn4)[C@@H]4OCCC[C@@H]43)c2c1) `ZINC001184490876.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490876/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184490876 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3C[C@H](NC(=O)c4cscn4)[C@@H]4OCCC[C@@H]43)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 14, 1, 8, 5, 7, 12, 5, 5, 5, 5, 7, 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, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 6, 6, 9, 9, 9, 9, 19, 19, 19, 21, 21, 21, 21, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 8, 8, 8, 5, 5, 5, 9, 9, 19, 21, 21, 9, 9, 9, 9, 9, 9, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490876 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490876 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490876/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490876/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490876 Building ZINC001184490930 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184490930 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 506) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/506 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/506' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4[C@H](C[C@@H](Cn5cncn5)N4CC4CC4)C3)c2c1) `ZINC001184490930.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184490930 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4[C@H](C[C@@H](Cn5cncn5)N4CC4CC4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.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, 5, 5, 5, 7, 5, 7, 5, 5, 7, 5, 8, 1, 8, 1, 8, 10, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 4, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 17, 23, 23, 23, 23, 10, 10, 12, 21, 21, 10, 3, 3, 5, 5, 5, 3, 3, 3, 10, 10, 10, 10, 10, 10, 17, 17, 23, 23, 12, 12, 21, 21, 21, 21, 21, 10, 10, 3] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 507) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/507 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/507' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4[C@H](C[C@@H](Cn5cncn5)N4CC4CC4)C3)c2c1) `ZINC001184490930.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184490930 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4[C@H](C[C@@H](Cn5cncn5)N4CC4CC4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.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, 5, 5, 5, 7, 5, 7, 5, 5, 7, 5, 8, 1, 8, 1, 8, 10, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 17, 17, 17, 17, 4, 4, 6, 11, 11, 4, 5, 5, 8, 8, 8, 5, 5, 5, 4, 4, 4, 4, 4, 4, 9, 9, 17, 17, 6, 6, 11, 11, 11, 11, 11, 4, 4, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 508) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/508 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/508' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4[C@H](C[C@@H](Cn5cncn5)N4CC4CC4)C3)c2c1) `ZINC001184490930.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184490930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184490930 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4[C@H](C[C@@H](Cn5cncn5)N4CC4CC4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.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, 5, 5, 5, 7, 5, 7, 5, 5, 7, 5, 8, 1, 8, 1, 8, 10, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 4, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 17, 23, 23, 23, 23, 10, 10, 12, 21, 21, 10, 3, 3, 5, 5, 5, 3, 3, 3, 10, 10, 10, 10, 10, 10, 17, 17, 23, 23, 12, 12, 21, 21, 21, 21, 21, 10, 10, 3] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 509) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/509 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/509' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4[C@H](C[C@@H](Cn5cncn5)N4CC4CC4)C3)c2c1) `ZINC001184490930.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184490930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184490930 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4[C@H](C[C@@H](Cn5cncn5)N4CC4CC4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.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, 5, 5, 5, 7, 5, 7, 5, 5, 7, 5, 8, 1, 8, 1, 8, 10, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 17, 17, 17, 17, 4, 4, 6, 11, 11, 4, 5, 5, 8, 8, 8, 5, 5, 5, 4, 4, 4, 4, 4, 4, 9, 9, 17, 17, 6, 6, 11, 11, 11, 11, 11, 4, 4, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490930 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930 Building ZINC001184490930 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184490930 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 506) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4[C@H](C[C@@H](Cn5cncn5)N4CC4CC4)C3)c2c1) `ZINC001184490930.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184490930 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4[C@H](C[C@@H](Cn5cncn5)N4CC4CC4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.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, 5, 5, 5, 7, 5, 7, 5, 5, 7, 5, 8, 1, 8, 1, 8, 10, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 4, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 17, 23, 23, 23, 23, 10, 10, 12, 21, 21, 10, 3, 3, 5, 5, 5, 3, 3, 3, 10, 10, 10, 10, 10, 10, 17, 17, 23, 23, 12, 12, 21, 21, 21, 21, 21, 10, 10, 3] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 507) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4[C@H](C[C@@H](Cn5cncn5)N4CC4CC4)C3)c2c1) `ZINC001184490930.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184490930 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4[C@H](C[C@@H](Cn5cncn5)N4CC4CC4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.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, 5, 5, 5, 7, 5, 7, 5, 5, 7, 5, 8, 1, 8, 1, 8, 10, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 17, 17, 17, 17, 4, 4, 6, 11, 11, 4, 5, 5, 8, 8, 8, 5, 5, 5, 4, 4, 4, 4, 4, 4, 9, 9, 17, 17, 6, 6, 11, 11, 11, 11, 11, 4, 4, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 508) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/508: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4[C@H](C[C@@H](Cn5cncn5)N4CC4CC4)C3)c2c1) `ZINC001184490930.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184490930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184490930 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4[C@H](C[C@@H](Cn5cncn5)N4CC4CC4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.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, 5, 5, 5, 7, 5, 7, 5, 5, 7, 5, 8, 1, 8, 1, 8, 10, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 4, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 17, 23, 23, 23, 23, 10, 10, 12, 21, 21, 10, 3, 3, 5, 5, 5, 3, 3, 3, 10, 10, 10, 10, 10, 10, 17, 17, 23, 23, 12, 12, 21, 21, 21, 21, 21, 10, 10, 3] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 509) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/509: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4[C@H](C[C@@H](Cn5cncn5)N4CC4CC4)C3)c2c1) `ZINC001184490930.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184490930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184490930 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4[C@H](C[C@@H](Cn5cncn5)N4CC4CC4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.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, 5, 5, 5, 7, 5, 7, 5, 5, 7, 5, 8, 1, 8, 1, 8, 10, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 17, 17, 17, 17, 4, 4, 6, 11, 11, 4, 5, 5, 8, 8, 8, 5, 5, 5, 4, 4, 4, 4, 4, 4, 9, 9, 17, 17, 6, 6, 11, 11, 11, 11, 11, 4, 4, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490930 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930 Building ZINC001184490930 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184490930 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 506) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4[C@H](C[C@@H](Cn5cncn5)N4CC4CC4)C3)c2c1) `ZINC001184490930.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184490930 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4[C@H](C[C@@H](Cn5cncn5)N4CC4CC4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.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, 5, 5, 5, 7, 5, 7, 5, 5, 7, 5, 8, 1, 8, 1, 8, 10, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 4, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 17, 23, 23, 23, 23, 10, 10, 12, 21, 21, 10, 3, 3, 5, 5, 5, 3, 3, 3, 10, 10, 10, 10, 10, 10, 17, 17, 23, 23, 12, 12, 21, 21, 21, 21, 21, 10, 10, 3] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 507) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4[C@H](C[C@@H](Cn5cncn5)N4CC4CC4)C3)c2c1) `ZINC001184490930.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184490930 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4[C@H](C[C@@H](Cn5cncn5)N4CC4CC4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.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, 5, 5, 5, 7, 5, 7, 5, 5, 7, 5, 8, 1, 8, 1, 8, 10, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 17, 17, 17, 17, 4, 4, 6, 11, 11, 4, 5, 5, 8, 8, 8, 5, 5, 5, 4, 4, 4, 4, 4, 4, 9, 9, 17, 17, 6, 6, 11, 11, 11, 11, 11, 4, 4, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 508) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/508: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4[C@H](C[C@@H](Cn5cncn5)N4CC4CC4)C3)c2c1) `ZINC001184490930.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184490930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184490930 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4[C@H](C[C@@H](Cn5cncn5)N4CC4CC4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.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, 5, 5, 5, 7, 5, 7, 5, 5, 7, 5, 8, 1, 8, 1, 8, 10, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 4, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 17, 23, 23, 23, 23, 10, 10, 12, 21, 21, 10, 3, 3, 5, 5, 5, 3, 3, 3, 10, 10, 10, 10, 10, 10, 17, 17, 23, 23, 12, 12, 21, 21, 21, 21, 21, 10, 10, 3] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 509) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/509: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4[C@H](C[C@@H](Cn5cncn5)N4CC4CC4)C3)c2c1) `ZINC001184490930.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184490930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184490930 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4[C@H](C[C@@H](Cn5cncn5)N4CC4CC4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.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, 5, 5, 5, 7, 5, 7, 5, 5, 7, 5, 8, 1, 8, 1, 8, 10, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 17, 17, 17, 17, 4, 4, 6, 11, 11, 4, 5, 5, 8, 8, 8, 5, 5, 5, 4, 4, 4, 4, 4, 4, 9, 9, 17, 17, 6, 6, 11, 11, 11, 11, 11, 4, 4, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490930 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930 Building ZINC001184490930 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184490930 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 506) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4[C@H](C[C@@H](Cn5cncn5)N4CC4CC4)C3)c2c1) `ZINC001184490930.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184490930 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4[C@H](C[C@@H](Cn5cncn5)N4CC4CC4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.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, 5, 5, 5, 7, 5, 7, 5, 5, 7, 5, 8, 1, 8, 1, 8, 10, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 4, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 17, 23, 23, 23, 23, 10, 10, 12, 21, 21, 10, 3, 3, 5, 5, 5, 3, 3, 3, 10, 10, 10, 10, 10, 10, 17, 17, 23, 23, 12, 12, 21, 21, 21, 21, 21, 10, 10, 3] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 507) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4[C@H](C[C@@H](Cn5cncn5)N4CC4CC4)C3)c2c1) `ZINC001184490930.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184490930 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4[C@H](C[C@@H](Cn5cncn5)N4CC4CC4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.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, 5, 5, 5, 7, 5, 7, 5, 5, 7, 5, 8, 1, 8, 1, 8, 10, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 17, 17, 17, 17, 4, 4, 6, 11, 11, 4, 5, 5, 8, 8, 8, 5, 5, 5, 4, 4, 4, 4, 4, 4, 9, 9, 17, 17, 6, 6, 11, 11, 11, 11, 11, 4, 4, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 508) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/508: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4[C@H](C[C@@H](Cn5cncn5)N4CC4CC4)C3)c2c1) `ZINC001184490930.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184490930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184490930 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4[C@H](C[C@@H](Cn5cncn5)N4CC4CC4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.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, 5, 5, 5, 7, 5, 7, 5, 5, 7, 5, 8, 1, 8, 1, 8, 10, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 4, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 17, 23, 23, 23, 23, 10, 10, 12, 21, 21, 10, 3, 3, 5, 5, 5, 3, 3, 3, 10, 10, 10, 10, 10, 10, 17, 17, 23, 23, 12, 12, 21, 21, 21, 21, 21, 10, 10, 3] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 509) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/509: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4[C@H](C[C@@H](Cn5cncn5)N4CC4CC4)C3)c2c1) `ZINC001184490930.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184490930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184490930 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4[C@H](C[C@@H](Cn5cncn5)N4CC4CC4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.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, 5, 5, 5, 7, 5, 7, 5, 5, 7, 5, 8, 1, 8, 1, 8, 10, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 17, 17, 17, 17, 4, 4, 6, 11, 11, 4, 5, 5, 8, 8, 8, 5, 5, 5, 4, 4, 4, 4, 4, 4, 9, 9, 17, 17, 6, 6, 11, 11, 11, 11, 11, 4, 4, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184490930 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184490930 Building ZINC001184491178 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491178' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491178 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184491178 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491178/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491178 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 510) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/510 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/510' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3C[C@@H]4COC[C@]4(C(=O)NCCc4cccs4)C3)c2c1) `ZINC001184491178.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491178/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491178 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3C[C@@H]4COC[C@]4(C(=O)NCCc4cccs4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.ar', 'C.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, 7, 5, 12, 5, 5, 1, 11, 8, 5, 5, 1, 1, 1, 1, 14, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 3, 8, 8, 8, 8, 8, 8, 8, 8, 11, 11, 11, 24, 34, 47, 47, 47, 47, 8, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 11, 24, 24, 34, 34, 47, 47, 47, 8, 8, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491178 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491178/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491178 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 511) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/511 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/511' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3C[C@@H]4COC[C@]4(C(=O)NCCc4cccs4)C3)c2c1) `ZINC001184491178.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491178/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491178 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3C[C@@H]4COC[C@]4(C(=O)NCCc4cccs4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.ar', 'C.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, 7, 5, 12, 5, 5, 1, 11, 8, 5, 5, 1, 1, 1, 1, 14, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 16, 22, 30, 30, 30, 30, 2, 3, 3, 4, 4, 4, 3, 3, 3, 2, 2, 2, 2, 2, 2, 4, 16, 16, 22, 22, 30, 30, 30, 2, 2, 3] 50 rigid atoms, others: [9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491178 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184491178 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491178/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491178/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491178 Building ZINC001184491178 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491178' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491178 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184491178 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491178/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491178 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 510) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3C[C@@H]4COC[C@]4(C(=O)NCCc4cccs4)C3)c2c1) `ZINC001184491178.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491178/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491178 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3C[C@@H]4COC[C@]4(C(=O)NCCc4cccs4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.ar', 'C.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, 7, 5, 12, 5, 5, 1, 11, 8, 5, 5, 1, 1, 1, 1, 14, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 3, 8, 8, 8, 8, 8, 8, 8, 8, 11, 11, 11, 24, 34, 47, 47, 47, 47, 8, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 11, 24, 24, 34, 34, 47, 47, 47, 8, 8, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491178 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491178/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491178 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 511) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3C[C@@H]4COC[C@]4(C(=O)NCCc4cccs4)C3)c2c1) `ZINC001184491178.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491178/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491178 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3C[C@@H]4COC[C@]4(C(=O)NCCc4cccs4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.ar', 'C.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, 7, 5, 12, 5, 5, 1, 11, 8, 5, 5, 1, 1, 1, 1, 14, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 16, 22, 30, 30, 30, 30, 2, 3, 3, 4, 4, 4, 3, 3, 3, 2, 2, 2, 2, 2, 2, 4, 16, 16, 22, 22, 30, 30, 30, 2, 2, 3] 50 rigid atoms, others: [9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491178 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184491178 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491178/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491178/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491178 Building ZINC001184491198 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491198' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491198 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184491198 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491198/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491198 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 512) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/512 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/512' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4OCC[C@@]4(C(=O)NCc4ccccn4)C3)c2c1) `ZINC001184491198.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491198 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4OCC[C@@]4(C(=O)NCc4ccccn4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 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: [7, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 3, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 23, 30, 30, 30, 30, 30, 5, 4, 4, 7, 7, 7, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 8, 23, 23, 30, 30, 30, 30, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491198 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491198/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491198 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 513) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/513 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/513' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4OCC[C@@]4(C(=O)NCc4ccccn4)C3)c2c1) `ZINC001184491198.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491198/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491198 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4OCC[C@@]4(C(=O)NCc4ccccn4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 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: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 8, 8, 24, 34, 34, 34, 34, 34, 7, 4, 4, 5, 5, 5, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 24, 24, 34, 34, 34, 34, 7, 7, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491198 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184491198 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491198/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491198/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491198 Building ZINC001184491198 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491198' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491198 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184491198 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491198/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491198 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 512) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4OCC[C@@]4(C(=O)NCc4ccccn4)C3)c2c1) `ZINC001184491198.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491198 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CC[C@H]4OCC[C@@]4(C(=O)NCc4ccccn4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 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: [7, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 3, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 23, 30, 30, 30, 30, 30, 5, 4, 4, 7, 7, 7, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 8, 23, 23, 30, 30, 30, 30, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491198 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491198/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491198 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 513) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4OCC[C@@]4(C(=O)NCc4ccccn4)C3)c2c1) `ZINC001184491198.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491198/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491198 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CC[C@H]4OCC[C@@]4(C(=O)NCc4ccccn4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 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: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 8, 8, 24, 34, 34, 34, 34, 34, 7, 4, 4, 5, 5, 5, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 24, 24, 34, 34, 34, 34, 7, 7, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491198 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184491198 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491198/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491198/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491198 Building ZINC001184491206 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184491206 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 514) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/514 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/514' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCCn4c(=O)cc(CN(C)C(C)C)nc4C3)c2c1) `ZINC001184491206.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491206 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCCn4c(=O)cc(CN(C)C(C)C)nc4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 10, 5, 5, 5, 5, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 3, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 20, 24, 24, 31, 31, 5, 5, 5, 4, 4, 5, 5, 5, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 20, 20, 24, 24, 24, 31, 31, 31, 31, 31, 31, 31, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 135 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 515) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/515 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/515' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCCn4c(=O)cc(CN(C)C(C)C)nc4C3)c2c1) `ZINC001184491206.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491206 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCCn4c(=O)cc(CN(C)C(C)C)nc4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 10, 5, 5, 5, 5, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 3, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 20, 24, 24, 31, 31, 5, 5, 5, 4, 4, 5, 5, 5, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 20, 20, 24, 24, 24, 31, 31, 31, 31, 31, 31, 31, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 135 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 516) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/516 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/516' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCCn4c(=O)cc(CN(C)C(C)C)nc4C3)c2c1) `ZINC001184491206.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184491206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491206 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCCn4c(=O)cc(CN(C)C(C)C)nc4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 10, 5, 5, 5, 5, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 3, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 20, 22, 22, 25, 25, 5, 5, 5, 4, 4, 5, 5, 5, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 20, 20, 22, 22, 22, 25, 25, 25, 25, 25, 25, 25, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 103 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 517) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/517 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/517' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCCn4c(=O)cc(CN(C)C(C)C)nc4C3)c2c1) `ZINC001184491206.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184491206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491206 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCCn4c(=O)cc(CN(C)C(C)C)nc4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 10, 5, 5, 5, 5, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 3, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 20, 22, 22, 25, 25, 5, 5, 5, 4, 4, 5, 5, 5, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 20, 20, 22, 22, 22, 25, 25, 25, 25, 25, 25, 25, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 103 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184491206 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206 Building ZINC001184491206 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184491206 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 514) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/514: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCCn4c(=O)cc(CN(C)C(C)C)nc4C3)c2c1) `ZINC001184491206.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491206 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCCn4c(=O)cc(CN(C)C(C)C)nc4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 10, 5, 5, 5, 5, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 3, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 20, 24, 24, 31, 31, 5, 5, 5, 4, 4, 5, 5, 5, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 20, 20, 24, 24, 24, 31, 31, 31, 31, 31, 31, 31, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 135 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 515) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/515: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCCn4c(=O)cc(CN(C)C(C)C)nc4C3)c2c1) `ZINC001184491206.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491206 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCCn4c(=O)cc(CN(C)C(C)C)nc4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 10, 5, 5, 5, 5, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 3, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 20, 24, 24, 31, 31, 5, 5, 5, 4, 4, 5, 5, 5, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 20, 20, 24, 24, 24, 31, 31, 31, 31, 31, 31, 31, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 135 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 516) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/516: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCCn4c(=O)cc(CN(C)C(C)C)nc4C3)c2c1) `ZINC001184491206.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184491206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491206 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCCn4c(=O)cc(CN(C)C(C)C)nc4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 10, 5, 5, 5, 5, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 3, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 20, 22, 22, 25, 25, 5, 5, 5, 4, 4, 5, 5, 5, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 20, 20, 22, 22, 22, 25, 25, 25, 25, 25, 25, 25, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 103 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 517) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/517: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCCn4c(=O)cc(CN(C)C(C)C)nc4C3)c2c1) `ZINC001184491206.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184491206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491206 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCCn4c(=O)cc(CN(C)C(C)C)nc4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 10, 5, 5, 5, 5, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 3, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 20, 22, 22, 25, 25, 5, 5, 5, 4, 4, 5, 5, 5, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 20, 20, 22, 22, 22, 25, 25, 25, 25, 25, 25, 25, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 103 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184491206 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206 Building ZINC001184491206 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184491206 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 514) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/514: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCCn4c(=O)cc(CN(C)C(C)C)nc4C3)c2c1) `ZINC001184491206.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491206 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCCn4c(=O)cc(CN(C)C(C)C)nc4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 10, 5, 5, 5, 5, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 3, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 20, 24, 24, 31, 31, 5, 5, 5, 4, 4, 5, 5, 5, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 20, 20, 24, 24, 24, 31, 31, 31, 31, 31, 31, 31, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 135 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 515) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/515: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCCn4c(=O)cc(CN(C)C(C)C)nc4C3)c2c1) `ZINC001184491206.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491206 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCCn4c(=O)cc(CN(C)C(C)C)nc4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 10, 5, 5, 5, 5, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 3, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 20, 24, 24, 31, 31, 5, 5, 5, 4, 4, 5, 5, 5, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 20, 20, 24, 24, 24, 31, 31, 31, 31, 31, 31, 31, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 135 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 516) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/516: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCCn4c(=O)cc(CN(C)C(C)C)nc4C3)c2c1) `ZINC001184491206.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184491206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491206 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCCn4c(=O)cc(CN(C)C(C)C)nc4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 10, 5, 5, 5, 5, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 3, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 20, 22, 22, 25, 25, 5, 5, 5, 4, 4, 5, 5, 5, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 20, 20, 22, 22, 22, 25, 25, 25, 25, 25, 25, 25, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 103 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 517) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/517: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCCn4c(=O)cc(CN(C)C(C)C)nc4C3)c2c1) `ZINC001184491206.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184491206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491206 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCCn4c(=O)cc(CN(C)C(C)C)nc4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 10, 5, 5, 5, 5, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 3, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 20, 22, 22, 25, 25, 5, 5, 5, 4, 4, 5, 5, 5, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 20, 20, 22, 22, 22, 25, 25, 25, 25, 25, 25, 25, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 103 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184491206 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206 Building ZINC001184491206 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184491206 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 514) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/514: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCCn4c(=O)cc(CN(C)C(C)C)nc4C3)c2c1) `ZINC001184491206.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491206 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCCn4c(=O)cc(CN(C)C(C)C)nc4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 10, 5, 5, 5, 5, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 3, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 20, 24, 24, 31, 31, 5, 5, 5, 4, 4, 5, 5, 5, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 20, 20, 24, 24, 24, 31, 31, 31, 31, 31, 31, 31, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 135 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 515) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/515: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCCn4c(=O)cc(CN(C)C(C)C)nc4C3)c2c1) `ZINC001184491206.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491206 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCCn4c(=O)cc(CN(C)C(C)C)nc4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 10, 5, 5, 5, 5, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 3, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 20, 24, 24, 31, 31, 5, 5, 5, 4, 4, 5, 5, 5, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 20, 20, 24, 24, 24, 31, 31, 31, 31, 31, 31, 31, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 135 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 516) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/516: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCCn4c(=O)cc(CN(C)C(C)C)nc4C3)c2c1) `ZINC001184491206.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184491206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491206 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCCn4c(=O)cc(CN(C)C(C)C)nc4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 10, 5, 5, 5, 5, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 3, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 20, 22, 22, 25, 25, 5, 5, 5, 4, 4, 5, 5, 5, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 20, 20, 22, 22, 22, 25, 25, 25, 25, 25, 25, 25, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 103 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 517) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/517: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCCn4c(=O)cc(CN(C)C(C)C)nc4C3)c2c1) `ZINC001184491206.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184491206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491206 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCCn4c(=O)cc(CN(C)C(C)C)nc4C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 5, 10, 5, 5, 5, 5, 8, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 3, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 20, 22, 22, 25, 25, 5, 5, 5, 4, 4, 5, 5, 5, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 20, 20, 22, 22, 22, 25, 25, 25, 25, 25, 25, 25, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 103 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184491206 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491206 Building ZINC001184491209 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491209' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491209 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184491209 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491209/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491209 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 518) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/518 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/518' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CC3)CN(Cc3cccnc3)C(=O)CO4)c2c1) `ZINC001184491209.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491209 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CC3)CN(Cc3cccnc3)C(=O)CO4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 8, 1, 1, 11, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 23, 39, 39, 39, 39, 39, 9, 9, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 23, 23, 39, 39, 39, 39, 9, 9, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491209 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491209/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491209 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 519) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/519 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/519' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CC3)CN(Cc3cccnc3)C(=O)CO4)c2c1) `ZINC001184491209.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491209/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491209 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CC3)CN(Cc3cccnc3)C(=O)CO4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 8, 1, 1, 11, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 6, 7, 7, 7, 25, 35, 35, 35, 35, 35, 7, 7, 7, 7, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 25, 25, 35, 35, 35, 35, 7, 7, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491209 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184491209 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491209/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491209/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491209 Building ZINC001184491209 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491209' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491209 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184491209 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491209/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491209 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 518) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CC3)CN(Cc3cccnc3)C(=O)CO4)c2c1) `ZINC001184491209.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491209 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CC3)CN(Cc3cccnc3)C(=O)CO4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 8, 1, 1, 11, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 23, 39, 39, 39, 39, 39, 9, 9, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 23, 23, 39, 39, 39, 39, 9, 9, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491209 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491209/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491209 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 519) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CC3)CN(Cc3cccnc3)C(=O)CO4)c2c1) `ZINC001184491209.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491209/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491209 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CC3)CN(Cc3cccnc3)C(=O)CO4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 8, 1, 1, 11, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 6, 7, 7, 7, 25, 35, 35, 35, 35, 35, 7, 7, 7, 7, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 25, 25, 35, 35, 35, 35, 7, 7, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491209 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184491209 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491209/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491209/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491209 Building ZINC001184491374 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184491374 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 520) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/520 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/520' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(N(C)C(=O)C[N@]4CC[N@](C)CC4)cc3)c2c1) `ZINC001184491374.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184491374 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(N(C)C(=O)C[N@]4CC[N@](C)CC4)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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', 'H', '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, 5, 1, 11, 5, 10, 5, 5, 10, 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, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 3, 3, 18, 18, 22, 22, 33, 34, 34, 34, 34, 34, 34, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 18, 18, 18, 33, 33, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 5, 5, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 521) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/521 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/521' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(N(C)C(=O)C[N@]4CC[N@@](C)CC4)cc3)c2c1) `ZINC001184491374.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184491374 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(N(C)C(=O)C[N@]4CC[N@@](C)CC4)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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', 'H', '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, 5, 1, 11, 5, 10, 5, 5, 10, 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, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 3, 5, 21, 21, 22, 22, 33, 34, 34, 34, 34, 34, 34, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 21, 21, 21, 33, 33, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 5, 5, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 522) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/522 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/522' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(N(C)C(=O)C[N@]4CC[N@](C)CC4)cc3)c2c1) `ZINC001184491374.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184491374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184491374 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(N(C)C(=O)C[N@]4CC[N@](C)CC4)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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', 'H', '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, 5, 1, 11, 5, 10, 5, 5, 10, 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, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 5, 20, 20, 21, 21, 35, 36, 36, 36, 36, 36, 36, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 20, 20, 20, 35, 35, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 523) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/523 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/523' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(N(C)C(=O)C[N@]4CC[N@@](C)CC4)cc3)c2c1) `ZINC001184491374.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184491374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184491374 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(N(C)C(=O)C[N@]4CC[N@@](C)CC4)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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', 'H', '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, 5, 1, 11, 5, 10, 5, 5, 10, 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, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 18, 18, 20, 20, 32, 34, 34, 34, 34, 34, 34, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 18, 18, 18, 32, 32, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184491374 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374 Building ZINC001184491374 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184491374 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 520) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(N(C)C(=O)C[N@]4CC[N@](C)CC4)cc3)c2c1) `ZINC001184491374.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184491374 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(N(C)C(=O)C[N@]4CC[N@](C)CC4)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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', 'H', '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, 5, 1, 11, 5, 10, 5, 5, 10, 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, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 3, 3, 18, 18, 22, 22, 33, 34, 34, 34, 34, 34, 34, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 18, 18, 18, 33, 33, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 5, 5, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 521) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(N(C)C(=O)C[N@]4CC[N@@](C)CC4)cc3)c2c1) `ZINC001184491374.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184491374 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(N(C)C(=O)C[N@]4CC[N@@](C)CC4)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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', 'H', '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, 5, 1, 11, 5, 10, 5, 5, 10, 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, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 3, 5, 21, 21, 22, 22, 33, 34, 34, 34, 34, 34, 34, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 21, 21, 21, 33, 33, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 5, 5, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 522) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/522: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(N(C)C(=O)C[N@]4CC[N@](C)CC4)cc3)c2c1) `ZINC001184491374.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184491374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184491374 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(N(C)C(=O)C[N@]4CC[N@](C)CC4)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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', 'H', '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, 5, 1, 11, 5, 10, 5, 5, 10, 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, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 5, 20, 20, 21, 21, 35, 36, 36, 36, 36, 36, 36, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 20, 20, 20, 35, 35, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 523) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/523: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(N(C)C(=O)C[N@]4CC[N@@](C)CC4)cc3)c2c1) `ZINC001184491374.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184491374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184491374 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(N(C)C(=O)C[N@]4CC[N@@](C)CC4)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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', 'H', '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, 5, 1, 11, 5, 10, 5, 5, 10, 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, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 18, 18, 20, 20, 32, 34, 34, 34, 34, 34, 34, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 18, 18, 18, 32, 32, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184491374 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374 Building ZINC001184491374 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184491374 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 520) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(N(C)C(=O)C[N@]4CC[N@](C)CC4)cc3)c2c1) `ZINC001184491374.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184491374 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(N(C)C(=O)C[N@]4CC[N@](C)CC4)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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', 'H', '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, 5, 1, 11, 5, 10, 5, 5, 10, 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, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 3, 3, 18, 18, 22, 22, 33, 34, 34, 34, 34, 34, 34, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 18, 18, 18, 33, 33, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 5, 5, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 521) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(N(C)C(=O)C[N@]4CC[N@@](C)CC4)cc3)c2c1) `ZINC001184491374.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184491374 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(N(C)C(=O)C[N@]4CC[N@@](C)CC4)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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', 'H', '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, 5, 1, 11, 5, 10, 5, 5, 10, 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, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 3, 5, 21, 21, 22, 22, 33, 34, 34, 34, 34, 34, 34, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 21, 21, 21, 33, 33, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 5, 5, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 522) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/522: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(N(C)C(=O)C[N@]4CC[N@](C)CC4)cc3)c2c1) `ZINC001184491374.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184491374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184491374 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(N(C)C(=O)C[N@]4CC[N@](C)CC4)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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', 'H', '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, 5, 1, 11, 5, 10, 5, 5, 10, 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, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 5, 20, 20, 21, 21, 35, 36, 36, 36, 36, 36, 36, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 20, 20, 20, 35, 35, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 523) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/523: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(N(C)C(=O)C[N@]4CC[N@@](C)CC4)cc3)c2c1) `ZINC001184491374.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184491374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184491374 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(N(C)C(=O)C[N@]4CC[N@@](C)CC4)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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', 'H', '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, 5, 1, 11, 5, 10, 5, 5, 10, 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, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 18, 18, 20, 20, 32, 34, 34, 34, 34, 34, 34, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 18, 18, 18, 32, 32, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184491374 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374 Building ZINC001184491374 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184491374 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 520) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(N(C)C(=O)C[N@]4CC[N@](C)CC4)cc3)c2c1) `ZINC001184491374.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184491374 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(N(C)C(=O)C[N@]4CC[N@](C)CC4)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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', 'H', '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, 5, 1, 11, 5, 10, 5, 5, 10, 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, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 3, 3, 18, 18, 22, 22, 33, 34, 34, 34, 34, 34, 34, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 18, 18, 18, 33, 33, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 5, 5, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 521) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(N(C)C(=O)C[N@]4CC[N@@](C)CC4)cc3)c2c1) `ZINC001184491374.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184491374 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(N(C)C(=O)C[N@]4CC[N@@](C)CC4)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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', 'H', '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, 5, 1, 11, 5, 10, 5, 5, 10, 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, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 3, 5, 21, 21, 22, 22, 33, 34, 34, 34, 34, 34, 34, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 21, 21, 21, 33, 33, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 5, 5, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 522) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/522: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(N(C)C(=O)C[N@]4CC[N@](C)CC4)cc3)c2c1) `ZINC001184491374.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184491374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184491374 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(N(C)C(=O)C[N@]4CC[N@](C)CC4)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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', 'H', '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, 5, 1, 11, 5, 10, 5, 5, 10, 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, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 5, 20, 20, 21, 21, 35, 36, 36, 36, 36, 36, 36, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 20, 20, 20, 35, 35, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 523) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/523: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(N(C)C(=O)C[N@]4CC[N@@](C)CC4)cc3)c2c1) `ZINC001184491374.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184491374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184491374 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(N(C)C(=O)C[N@]4CC[N@@](C)CC4)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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', 'H', '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, 5, 1, 11, 5, 10, 5, 5, 10, 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, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 18, 18, 20, 20, 32, 34, 34, 34, 34, 34, 34, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 18, 18, 18, 32, 32, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184491374 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491374 Building ZINC001184491409 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491409' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491409 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184491409 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491409/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491409 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 524) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/524 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/524' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NCc3cc(=O)n4c(n3)CN(C(=O)OC(C)(C)C)CCC4)c2c1) `ZINC001184491409.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184491409 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NCc3cc(=O)n4c(n3)CN(C(=O)OC(C)(C)C)CCC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 11, 8, 1, 8, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 15, 23, 23, 23, 23, 23, 22, 23, 23, 23, 29, 29, 31, 31, 31, 31, 23, 23, 23, 4, 4, 4, 4, 4, 4, 4, 4, 3, 15, 15, 23, 23, 23, 31, 31, 31, 31, 31, 31, 31, 31, 31, 23, 23, 23, 23, 23, 23, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491409 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491409/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491409 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 525) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/525 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/525' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NCc3cc(=O)n4c(n3)CN(C(=O)OC(C)(C)C)CCC4)c2c1) `ZINC001184491409.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491409/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184491409 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NCc3cc(=O)n4c(n3)CN(C(=O)OC(C)(C)C)CCC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 11, 8, 1, 8, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 18, 27, 27, 27, 27, 27, 26, 27, 27, 27, 32, 32, 33, 33, 33, 33, 27, 27, 27, 4, 4, 4, 4, 4, 4, 4, 4, 3, 18, 18, 27, 27, 27, 33, 33, 33, 33, 33, 33, 33, 33, 33, 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, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491409 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184491409 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491409/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491409/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491409 Building ZINC001184491409 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491409' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491409 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184491409 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491409/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491409 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 524) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NCc3cc(=O)n4c(n3)CN(C(=O)OC(C)(C)C)CCC4)c2c1) `ZINC001184491409.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184491409 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NCc3cc(=O)n4c(n3)CN(C(=O)OC(C)(C)C)CCC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 11, 8, 1, 8, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 15, 23, 23, 23, 23, 23, 22, 23, 23, 23, 29, 29, 31, 31, 31, 31, 23, 23, 23, 4, 4, 4, 4, 4, 4, 4, 4, 3, 15, 15, 23, 23, 23, 31, 31, 31, 31, 31, 31, 31, 31, 31, 23, 23, 23, 23, 23, 23, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491409 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491409/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491409 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 525) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NCc3cc(=O)n4c(n3)CN(C(=O)OC(C)(C)C)CCC4)c2c1) `ZINC001184491409.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491409/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184491409 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NCc3cc(=O)n4c(n3)CN(C(=O)OC(C)(C)C)CCC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 11, 8, 1, 8, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 18, 27, 27, 27, 27, 27, 26, 27, 27, 27, 32, 32, 33, 33, 33, 33, 27, 27, 27, 4, 4, 4, 4, 4, 4, 4, 4, 3, 18, 18, 27, 27, 27, 33, 33, 33, 33, 33, 33, 33, 33, 33, 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, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491409 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184491409 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491409/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491409/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491409 Building ZINC001184491421 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491421' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491421 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184491421 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491421/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491421 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 526) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/526 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/526' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@H]3CCc4c(ccc(=O)n4CCn4cccn4)C3)c2c1) `ZINC001184491421.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184491421 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@H]3CCc4c(ccc(=O)n4CCn4cccn4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 1, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 21, 21, 34, 34, 34, 34, 12, 4, 4, 4, 4, 4, 4, 4, 4, 3, 12, 12, 12, 12, 12, 12, 21, 21, 21, 21, 34, 34, 34, 12, 12, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491421 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491421/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491421 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 527) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/527 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/527' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@H]3CCc4c(ccc(=O)n4CCn4cccn4)C3)c2c1) `ZINC001184491421.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491421/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184491421 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@H]3CCc4c(ccc(=O)n4CCn4cccn4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 1, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 21, 21, 34, 34, 34, 34, 13, 4, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 13, 13, 13, 13, 21, 21, 21, 21, 34, 34, 34, 13, 13, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491421 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184491421 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491421/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491421/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491421 Building ZINC001184491421 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491421' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491421 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184491421 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491421/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491421 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 526) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@H]3CCc4c(ccc(=O)n4CCn4cccn4)C3)c2c1) `ZINC001184491421.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184491421 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@H]3CCc4c(ccc(=O)n4CCn4cccn4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 1, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 21, 21, 34, 34, 34, 34, 12, 4, 4, 4, 4, 4, 4, 4, 4, 3, 12, 12, 12, 12, 12, 12, 21, 21, 21, 21, 34, 34, 34, 12, 12, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491421 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491421/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491421 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 527) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@H]3CCc4c(ccc(=O)n4CCn4cccn4)C3)c2c1) `ZINC001184491421.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491421/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184491421 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@H]3CCc4c(ccc(=O)n4CCn4cccn4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 1, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 21, 21, 34, 34, 34, 34, 13, 4, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 13, 13, 13, 13, 21, 21, 21, 21, 34, 34, 34, 13, 13, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491421 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184491421 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491421/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491421/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491421 Building ZINC001184491422 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491422' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491422 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184491422 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491422/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491422 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 528) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/528 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/528' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@@H]3CCc4c(ccc(=O)n4CCn4cccn4)C3)c2c1) `ZINC001184491422.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184491422 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@@H]3CCc4c(ccc(=O)n4CCn4cccn4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 1, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 21, 21, 34, 34, 34, 34, 13, 4, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 13, 13, 13, 13, 21, 21, 21, 21, 34, 34, 34, 13, 13, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491422 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491422/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491422 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 529) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/529 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/529' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@@H]3CCc4c(ccc(=O)n4CCn4cccn4)C3)c2c1) `ZINC001184491422.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491422/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184491422 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@@H]3CCc4c(ccc(=O)n4CCn4cccn4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 1, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 20, 20, 34, 34, 34, 34, 11, 4, 4, 4, 4, 4, 4, 4, 4, 3, 11, 11, 11, 11, 11, 11, 20, 20, 20, 20, 34, 34, 34, 11, 11, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491422 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184491422 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491422/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491422/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491422 Building ZINC001184491422 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491422' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491422 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184491422 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491422/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491422 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 528) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@@H]3CCc4c(ccc(=O)n4CCn4cccn4)C3)c2c1) `ZINC001184491422.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184491422 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@@H]3CCc4c(ccc(=O)n4CCn4cccn4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 1, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 21, 21, 34, 34, 34, 34, 13, 4, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 13, 13, 13, 13, 21, 21, 21, 21, 34, 34, 34, 13, 13, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491422 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491422/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491422 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 529) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@@H]3CCc4c(ccc(=O)n4CCn4cccn4)C3)c2c1) `ZINC001184491422.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491422/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184491422 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@@H]3CCc4c(ccc(=O)n4CCn4cccn4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 1, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 20, 20, 34, 34, 34, 34, 11, 4, 4, 4, 4, 4, 4, 4, 4, 3, 11, 11, 11, 11, 11, 11, 20, 20, 20, 20, 34, 34, 34, 11, 11, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491422 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184491422 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491422/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491422/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184491422 Building ZINC001184493018 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493018' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493018 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184493018 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493018/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493018 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 530) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/530 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/530' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)CCN(C(=O)OC(C)(C)C)CC1) `ZINC001184493018.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184493018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184493018 none COC(=O)C1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)CCN(C(=O)OC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 25, 7, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 19, 19, 19, 19, 25, 25, 26, 26, 26, 26, 19, 19, 25, 25, 25, 3, 3, 3, 3, 3, 3, 3, 3, 19, 19, 19, 19, 26, 26, 26, 26, 26, 26, 26, 26, 26, 19, 19, 19, 19] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493018 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493018/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493018 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 531) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/531 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/531' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)CCN(C(=O)OC(C)(C)C)CC1) `ZINC001184493018.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184493018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493018/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184493018 none COC(=O)C1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)CCN(C(=O)OC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 17, 24, 7, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 17, 17, 17, 17, 22, 22, 24, 24, 24, 24, 17, 17, 24, 24, 24, 3, 3, 3, 3, 3, 3, 3, 3, 17, 17, 17, 17, 24, 24, 24, 24, 24, 24, 24, 24, 24, 17, 17, 17, 17] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493018 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184493018 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493018/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493018/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493018 Building ZINC001184493018 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493018' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493018 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184493018 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493018/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493018 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 530) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COC(=O)C1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)CCN(C(=O)OC(C)(C)C)CC1) `ZINC001184493018.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184493018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184493018 none COC(=O)C1(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)CCN(C(=O)OC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 25, 7, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 19, 19, 19, 19, 25, 25, 26, 26, 26, 26, 19, 19, 25, 25, 25, 3, 3, 3, 3, 3, 3, 3, 3, 19, 19, 19, 19, 26, 26, 26, 26, 26, 26, 26, 26, 26, 19, 19, 19, 19] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493018 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493018/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493018 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 531) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COC(=O)C1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)CCN(C(=O)OC(C)(C)C)CC1) `ZINC001184493018.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184493018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493018/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184493018 none COC(=O)C1(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)CCN(C(=O)OC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 17, 24, 7, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 17, 17, 17, 17, 22, 22, 24, 24, 24, 24, 17, 17, 24, 24, 24, 3, 3, 3, 3, 3, 3, 3, 3, 17, 17, 17, 17, 24, 24, 24, 24, 24, 24, 24, 24, 24, 17, 17, 17, 17] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493018 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184493018 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493018/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493018/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493018 Building ZINC001184493179 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493179' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493179 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184493179 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493179/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493179 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 532) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/532 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/532' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NC[C@H]3CN(c4ccc(N5CCOCC5)c(F)c4)C(=O)O3)c2c1) `ZINC001184493179.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184493179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184493179 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NC[C@H]3CN(c4ccc(N5CCOCC5)c(F)c4)C(=O)O3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 15, 1, 1, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 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, 15, 15, 15, 15, 22, 22, 22, 22, 39, 39, 39, 39, 39, 22, 22, 22, 15, 15, 15, 4, 4, 4, 4, 4, 4, 4, 4, 3, 8, 8, 15, 15, 22, 22, 39, 39, 39, 39, 39, 39, 39, 39, 22, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493179 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493179/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493179 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 533) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/533 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/533' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NC[C@H]3CN(c4ccc(N5CCOCC5)c(F)c4)C(=O)O3)c2c1) `ZINC001184493179.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184493179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493179/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184493179 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NC[C@H]3CN(c4ccc(N5CCOCC5)c(F)c4)C(=O)O3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 15, 1, 1, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in 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, 12, 15, 15, 15, 15, 21, 21, 21, 21, 36, 36, 36, 36, 36, 21, 21, 21, 15, 15, 15, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 15, 15, 21, 21, 36, 36, 36, 36, 36, 36, 36, 36, 21, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493179 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184493179 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493179/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493179/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493179 Building ZINC001184493179 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493179' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493179 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184493179 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493179/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493179 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 532) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NC[C@H]3CN(c4ccc(N5CCOCC5)c(F)c4)C(=O)O3)c2c1) `ZINC001184493179.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184493179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184493179 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NC[C@H]3CN(c4ccc(N5CCOCC5)c(F)c4)C(=O)O3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 15, 1, 1, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 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, 15, 15, 15, 15, 22, 22, 22, 22, 39, 39, 39, 39, 39, 22, 22, 22, 15, 15, 15, 4, 4, 4, 4, 4, 4, 4, 4, 3, 8, 8, 15, 15, 22, 22, 39, 39, 39, 39, 39, 39, 39, 39, 22, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493179 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493179/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493179 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 533) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NC[C@H]3CN(c4ccc(N5CCOCC5)c(F)c4)C(=O)O3)c2c1) `ZINC001184493179.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184493179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493179/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001184493179 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NC[C@H]3CN(c4ccc(N5CCOCC5)c(F)c4)C(=O)O3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 15, 1, 1, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in 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, 12, 15, 15, 15, 15, 21, 21, 21, 21, 36, 36, 36, 36, 36, 21, 21, 21, 15, 15, 15, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 15, 15, 21, 21, 36, 36, 36, 36, 36, 36, 36, 36, 21, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493179 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184493179 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493179/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493179/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493179 Building ZINC001184493632 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493632' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493632 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184493632 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493632/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493632 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 534) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/534 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/534' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3c(=O)n(C)nc(Cl)c3I)c2c1) `ZINC001184493632.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184493632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001184493632 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3c(=O)n(C)nc(Cl)c3I)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', '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', 'O.2', 'N.am', 'C.3', 'N.2', 'C.2', 'Cl', 'C.2', 'I', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 11, 8, 5, 8, 1, 16, 1, 18, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 7, 11, 11, 11, 7, 7, 7, 6, 17, 17, 17, 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]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493632 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493632/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493632 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 535) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/535 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/535' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3c(=O)n(C)nc(Cl)c3I)c2c1) `ZINC001184493632.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184493632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493632/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001184493632 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3c(=O)n(C)nc(Cl)c3I)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', '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', 'O.2', 'N.am', 'C.3', 'N.2', 'C.2', 'Cl', 'C.2', 'I', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 11, 8, 5, 8, 1, 16, 1, 18, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 7, 10, 10, 10, 7, 7, 7, 6, 17, 17, 17, 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]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493632 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184493632 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493632/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493632/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493632 Building ZINC001184493632 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493632' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493632 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184493632 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493632/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493632 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 534) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3c(=O)n(C)nc(Cl)c3I)c2c1) `ZINC001184493632.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184493632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001184493632 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3c(=O)n(C)nc(Cl)c3I)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', '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', 'O.2', 'N.am', 'C.3', 'N.2', 'C.2', 'Cl', 'C.2', 'I', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 11, 8, 5, 8, 1, 16, 1, 18, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 7, 11, 11, 11, 7, 7, 7, 6, 17, 17, 17, 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]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493632 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493632/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493632 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 535) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3c(=O)n(C)nc(Cl)c3I)c2c1) `ZINC001184493632.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184493632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493632/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001184493632 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3c(=O)n(C)nc(Cl)c3I)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', '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', 'O.2', 'N.am', 'C.3', 'N.2', 'C.2', 'Cl', 'C.2', 'I', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 11, 8, 5, 8, 1, 16, 1, 18, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 7, 10, 10, 10, 7, 7, 7, 6, 17, 17, 17, 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]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493632 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184493632 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493632/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493632/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493632 Building ZINC001184493858 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493858' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493858 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184493858 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493858/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493858 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 536) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/536 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/536' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@H]3CC(=O)N(Cc4ccc(OC)cc4OC)C3)c2c1) `ZINC001184493858.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184493858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184493858 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@H]3CC(=O)N(Cc4ccc(OC)cc4OC)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 12, 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, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 6, 16, 16, 16, 16, 16, 16, 26, 30, 30, 26, 30, 32, 30, 30, 30, 31, 16, 4, 4, 4, 4, 4, 4, 4, 4, 3, 16, 16, 26, 26, 30, 30, 32, 32, 32, 30, 31, 31, 31, 16, 16, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493858 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493858/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493858 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 537) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/537 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/537' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@H]3CC(=O)N(Cc4ccc(OC)cc4OC)C3)c2c1) `ZINC001184493858.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184493858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493858/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184493858 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@H]3CC(=O)N(Cc4ccc(OC)cc4OC)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 12, 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, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 6, 13, 13, 13, 13, 13, 13, 25, 35, 35, 26, 35, 39, 35, 35, 35, 38, 13, 4, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 25, 25, 35, 35, 39, 39, 39, 35, 38, 38, 38, 13, 13, 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]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493858 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184493858 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493858/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493858/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493858 Building ZINC001184493858 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493858' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493858 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184493858 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493858/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493858 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 536) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@H]3CC(=O)N(Cc4ccc(OC)cc4OC)C3)c2c1) `ZINC001184493858.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184493858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184493858 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N[C@H]3CC(=O)N(Cc4ccc(OC)cc4OC)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 12, 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, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 6, 16, 16, 16, 16, 16, 16, 26, 30, 30, 26, 30, 32, 30, 30, 30, 31, 16, 4, 4, 4, 4, 4, 4, 4, 4, 3, 16, 16, 26, 26, 30, 30, 32, 32, 32, 30, 31, 31, 31, 16, 16, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493858 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493858/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493858 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 537) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@H]3CC(=O)N(Cc4ccc(OC)cc4OC)C3)c2c1) `ZINC001184493858.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184493858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493858/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184493858 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N[C@H]3CC(=O)N(Cc4ccc(OC)cc4OC)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 12, 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, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 6, 13, 13, 13, 13, 13, 13, 25, 35, 35, 26, 35, 39, 35, 35, 35, 38, 13, 4, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 25, 25, 35, 35, 39, 39, 39, 35, 38, 38, 38, 13, 13, 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]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493858 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184493858 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493858/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493858/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493858 Building ZINC001184493956 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493956' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493956 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184493956 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493956/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493956 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 538) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/538 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/538' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](Cc1ccc(Br)cn1)NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21) `ZINC001184493956.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184493956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493956/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184493956 none COC(=O)[C@H](Cc1ccc(Br)cn1)NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 1, 1, 1, 1, 17, 1, 8, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 18, 4, 10, 10, 19, 20, 20, 20, 20, 20, 20, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 7, 6, 6, 18, 18, 18, 19, 19, 20, 20, 20, 4, 6, 6, 6, 7, 7, 7, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493956 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493956/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493956 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 539) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/539 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/539' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](Cc1ccc(Br)cn1)NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21) `ZINC001184493956.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184493956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493956/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184493956 none COC(=O)[C@H](Cc1ccc(Br)cn1)NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 1, 1, 1, 1, 17, 1, 8, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 16, 4, 9, 9, 15, 15, 15, 15, 15, 15, 15, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 16, 16, 16, 15, 15, 15, 15, 15, 4, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/418326/xbt-8058088.46/working/building/ZINC001184493956 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184493956 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493956/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493956/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493956 Building ZINC001184493956 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493956' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493956 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184493956 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493956/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493956 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 538) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COC(=O)[C@H](Cc1ccc(Br)cn1)NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21) `ZINC001184493956.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184493956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493956/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184493956 none COC(=O)[C@H](Cc1ccc(Br)cn1)NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 1, 1, 1, 1, 17, 1, 8, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 18, 4, 10, 10, 19, 20, 20, 20, 20, 20, 20, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 7, 6, 6, 18, 18, 18, 19, 19, 20, 20, 20, 4, 6, 6, 6, 7, 7, 7, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493956 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493956/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493956 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 539) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COC(=O)[C@H](Cc1ccc(Br)cn1)NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21) `ZINC001184493956.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184493956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493956/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184493956 none COC(=O)[C@H](Cc1ccc(Br)cn1)NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 1, 1, 1, 1, 17, 1, 8, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 16, 4, 9, 9, 15, 15, 15, 15, 15, 15, 15, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 16, 16, 16, 15, 15, 15, 15, 15, 4, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/418326/xbt-8058088.46/working/building/ZINC001184493956 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184493956 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493956/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493956/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184493956 Building ZINC001184495175 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184495175' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184495175 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184495175 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184495175/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184495175 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 540) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/540 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/540' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NCCOCCOCCOCCC(=O)OC(C)(C)C)c2c1) `ZINC001184495175.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184495175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184495175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184495175 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NCCOCCOCCOCCC(=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.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 5, 12, 5, 5, 1, 11, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 13, 13, 17, 17, 17, 20, 25, 32, 42, 42, 42, 42, 42, 42, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 2, 2, 2, 13, 13, 13, 13, 17, 17, 17, 17, 25, 25, 32, 32, 42, 42, 42, 42, 42, 42, 42, 42, 42, 2] 50 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 41] 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184495175 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184495175/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184495175 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 541) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/541 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/541' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NCCOCCOCCOCCC(=O)OC(C)(C)C)c2c1) `ZINC001184495175.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184495175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184495175/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184495175 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NCCOCCOCCOCCC(=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.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 5, 12, 5, 5, 1, 11, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 13, 13, 17, 17, 17, 20, 26, 33, 43, 43, 43, 43, 43, 43, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 2, 2, 2, 13, 13, 13, 13, 17, 17, 17, 17, 26, 26, 33, 33, 43, 43, 43, 43, 43, 43, 43, 43, 43, 2] 50 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 41] 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184495175 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184495175 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184495175/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184495175/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184495175 Building ZINC001184495175 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184495175' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184495175 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184495175 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184495175/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184495175 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 540) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/540: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NCCOCCOCCOCCC(=O)OC(C)(C)C)c2c1) `ZINC001184495175.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184495175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184495175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184495175 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NCCOCCOCCOCCC(=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.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 5, 12, 5, 5, 1, 11, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 13, 13, 17, 17, 17, 20, 25, 32, 42, 42, 42, 42, 42, 42, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 2, 2, 2, 13, 13, 13, 13, 17, 17, 17, 17, 25, 25, 32, 32, 42, 42, 42, 42, 42, 42, 42, 42, 42, 2] 50 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 41] 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184495175 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184495175/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184495175 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 541) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/541: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NCCOCCOCCOCCC(=O)OC(C)(C)C)c2c1) `ZINC001184495175.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184495175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184495175/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001184495175 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NCCOCCOCCOCCC(=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.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 5, 12, 5, 5, 1, 11, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 13, 13, 17, 17, 17, 20, 26, 33, 43, 43, 43, 43, 43, 43, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 2, 2, 2, 13, 13, 13, 13, 17, 17, 17, 17, 26, 26, 33, 33, 43, 43, 43, 43, 43, 43, 43, 43, 43, 2] 50 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 41] 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184495175 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001184495175 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184495175/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184495175/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001184495175 Building ZINC001219726420 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001219726420 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 542) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/542 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/542' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)NC[C@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O) `ZINC001219726420.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001219726420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001219726420 none COc1cc(C[C@@]([O-])([SiH3])C(=O)NC[C@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 3, 3, 3, 2, 1, 1, 1, 1, 1, 1, 1, 11, 22, 22, 22, 22, 34, 37, 37, 34, 37, 37, 22, 22, 22, 22, 22, 22, 22, 3, 3, 3, 3, 6, 6, 6, 3, 2, 2, 1, 7, 7, 22, 22, 34, 34, 37, 37, 36, 37, 37, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 3, 3, 6] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 40] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 543) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/543 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/543' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)NC[C@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O) `ZINC001219726420.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001219726420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001219726420 none COc1cc(C[C@]([O-])([SiH3])C(=O)NC[C@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 15, 15, 15, 15, 26, 33, 33, 26, 33, 33, 15, 15, 15, 15, 15, 15, 15, 3, 3, 3, 3, 5, 5, 5, 3, 2, 2, 1, 5, 5, 15, 15, 26, 26, 33, 33, 26, 33, 33, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 3, 3, 6] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 40] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 544) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/544 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/544' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)NC[C@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O) `ZINC001219726420.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001219726420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001219726420 none COc1cc(C[C@@]([O-])([SiH3])C(=O)NC[C@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 3, 3, 3, 2, 1, 1, 1, 1, 1, 1, 1, 11, 22, 22, 22, 22, 34, 37, 37, 34, 37, 37, 22, 22, 22, 22, 22, 22, 22, 3, 3, 3, 3, 6, 6, 6, 3, 2, 2, 1, 7, 7, 22, 22, 34, 34, 37, 37, 36, 37, 37, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 3, 3, 6] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 40] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 545) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/545 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/545' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)NC[C@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O) `ZINC001219726420.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001219726420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001219726420 none COc1cc(C[C@]([O-])([SiH3])C(=O)NC[C@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 15, 15, 15, 15, 26, 33, 33, 26, 33, 33, 15, 15, 15, 15, 15, 15, 15, 3, 3, 3, 3, 5, 5, 5, 3, 2, 2, 1, 5, 5, 15, 15, 26, 26, 33, 33, 26, 33, 33, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 3, 3, 6] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 40] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001219726420 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420 Building ZINC001219726420 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001219726420 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 542) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)NC[C@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O) `ZINC001219726420.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001219726420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001219726420 none COc1cc(C[C@@]([O-])([SiH3])C(=O)NC[C@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 3, 3, 3, 2, 1, 1, 1, 1, 1, 1, 1, 11, 22, 22, 22, 22, 34, 37, 37, 34, 37, 37, 22, 22, 22, 22, 22, 22, 22, 3, 3, 3, 3, 6, 6, 6, 3, 2, 2, 1, 7, 7, 22, 22, 34, 34, 37, 37, 36, 37, 37, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 3, 3, 6] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 40] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 543) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)NC[C@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O) `ZINC001219726420.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001219726420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001219726420 none COc1cc(C[C@]([O-])([SiH3])C(=O)NC[C@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 15, 15, 15, 15, 26, 33, 33, 26, 33, 33, 15, 15, 15, 15, 15, 15, 15, 3, 3, 3, 3, 5, 5, 5, 3, 2, 2, 1, 5, 5, 15, 15, 26, 26, 33, 33, 26, 33, 33, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 3, 3, 6] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 40] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 544) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/544: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O) `ZINC001219726420.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001219726420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001219726420 none COc1cc(C[C@@]([O-])([SiH3])C(=O)NC[C@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 3, 3, 3, 2, 1, 1, 1, 1, 1, 1, 1, 11, 22, 22, 22, 22, 34, 37, 37, 34, 37, 37, 22, 22, 22, 22, 22, 22, 22, 3, 3, 3, 3, 6, 6, 6, 3, 2, 2, 1, 7, 7, 22, 22, 34, 34, 37, 37, 36, 37, 37, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 3, 3, 6] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 40] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 545) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/545: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O) `ZINC001219726420.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001219726420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001219726420 none COc1cc(C[C@]([O-])([SiH3])C(=O)NC[C@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 15, 15, 15, 15, 26, 33, 33, 26, 33, 33, 15, 15, 15, 15, 15, 15, 15, 3, 3, 3, 3, 5, 5, 5, 3, 2, 2, 1, 5, 5, 15, 15, 26, 26, 33, 33, 26, 33, 33, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 3, 3, 6] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 40] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001219726420 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420 Building ZINC001219726420 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001219726420 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 542) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)NC[C@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O) `ZINC001219726420.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001219726420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001219726420 none COc1cc(C[C@@]([O-])([SiH3])C(=O)NC[C@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 3, 3, 3, 2, 1, 1, 1, 1, 1, 1, 1, 11, 22, 22, 22, 22, 34, 37, 37, 34, 37, 37, 22, 22, 22, 22, 22, 22, 22, 3, 3, 3, 3, 6, 6, 6, 3, 2, 2, 1, 7, 7, 22, 22, 34, 34, 37, 37, 36, 37, 37, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 3, 3, 6] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 40] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 543) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)NC[C@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O) `ZINC001219726420.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001219726420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001219726420 none COc1cc(C[C@]([O-])([SiH3])C(=O)NC[C@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 15, 15, 15, 15, 26, 33, 33, 26, 33, 33, 15, 15, 15, 15, 15, 15, 15, 3, 3, 3, 3, 5, 5, 5, 3, 2, 2, 1, 5, 5, 15, 15, 26, 26, 33, 33, 26, 33, 33, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 3, 3, 6] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 40] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 544) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/544: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O) `ZINC001219726420.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001219726420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001219726420 none COc1cc(C[C@@]([O-])([SiH3])C(=O)NC[C@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 3, 3, 3, 2, 1, 1, 1, 1, 1, 1, 1, 11, 22, 22, 22, 22, 34, 37, 37, 34, 37, 37, 22, 22, 22, 22, 22, 22, 22, 3, 3, 3, 3, 6, 6, 6, 3, 2, 2, 1, 7, 7, 22, 22, 34, 34, 37, 37, 36, 37, 37, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 3, 3, 6] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 40] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 545) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/545: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O) `ZINC001219726420.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001219726420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001219726420 none COc1cc(C[C@]([O-])([SiH3])C(=O)NC[C@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 15, 15, 15, 15, 26, 33, 33, 26, 33, 33, 15, 15, 15, 15, 15, 15, 15, 3, 3, 3, 3, 5, 5, 5, 3, 2, 2, 1, 5, 5, 15, 15, 26, 26, 33, 33, 26, 33, 33, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 3, 3, 6] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 40] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001219726420 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420 Building ZINC001219726420 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001219726420 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 542) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)NC[C@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O) `ZINC001219726420.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001219726420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001219726420 none COc1cc(C[C@@]([O-])([SiH3])C(=O)NC[C@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 3, 3, 3, 2, 1, 1, 1, 1, 1, 1, 1, 11, 22, 22, 22, 22, 34, 37, 37, 34, 37, 37, 22, 22, 22, 22, 22, 22, 22, 3, 3, 3, 3, 6, 6, 6, 3, 2, 2, 1, 7, 7, 22, 22, 34, 34, 37, 37, 36, 37, 37, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 3, 3, 6] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 40] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 543) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)NC[C@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O) `ZINC001219726420.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001219726420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001219726420 none COc1cc(C[C@]([O-])([SiH3])C(=O)NC[C@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 15, 15, 15, 15, 26, 33, 33, 26, 33, 33, 15, 15, 15, 15, 15, 15, 15, 3, 3, 3, 3, 5, 5, 5, 3, 2, 2, 1, 5, 5, 15, 15, 26, 26, 33, 33, 26, 33, 33, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 3, 3, 6] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 40] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 544) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/544: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O) `ZINC001219726420.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001219726420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001219726420 none COc1cc(C[C@@]([O-])([SiH3])C(=O)NC[C@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 3, 3, 3, 2, 1, 1, 1, 1, 1, 1, 1, 11, 22, 22, 22, 22, 34, 37, 37, 34, 37, 37, 22, 22, 22, 22, 22, 22, 22, 3, 3, 3, 3, 6, 6, 6, 3, 2, 2, 1, 7, 7, 22, 22, 34, 34, 37, 37, 36, 37, 37, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 3, 3, 6] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 40] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 545) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/545: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O) `ZINC001219726420.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001219726420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001219726420 none COc1cc(C[C@]([O-])([SiH3])C(=O)NC[C@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 15, 15, 15, 15, 26, 33, 33, 26, 33, 33, 15, 15, 15, 15, 15, 15, 15, 3, 3, 3, 3, 5, 5, 5, 3, 2, 2, 1, 5, 5, 15, 15, 26, 26, 33, 33, 26, 33, 33, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 3, 3, 6] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 40] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001219726420 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726420 Building ZINC001219726421 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001219726421 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 546) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/546 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/546' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)NC[C@@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O) `ZINC001219726421.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001219726421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001219726421 none COc1cc(C[C@@]([O-])([SiH3])C(=O)NC[C@@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 15, 15, 15, 15, 27, 34, 34, 29, 34, 34, 15, 15, 15, 15, 15, 15, 15, 3, 3, 3, 3, 5, 5, 5, 3, 2, 2, 1, 5, 5, 15, 15, 27, 27, 34, 34, 34, 34, 34, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 3, 3, 6] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 40] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 547) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/547 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/547' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)NC[C@@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O) `ZINC001219726421.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001219726421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001219726421 none COc1cc(C[C@]([O-])([SiH3])C(=O)NC[C@@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 3, 3, 3, 2, 1, 1, 1, 1, 1, 1, 1, 11, 22, 22, 22, 22, 34, 37, 37, 35, 37, 37, 22, 22, 22, 22, 22, 22, 22, 3, 3, 3, 3, 6, 6, 6, 3, 2, 2, 1, 7, 7, 22, 22, 34, 34, 37, 37, 37, 37, 37, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 3, 3, 6] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 40] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 548) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/548 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/548' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)NC[C@@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O) `ZINC001219726421.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001219726421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001219726421 none COc1cc(C[C@@]([O-])([SiH3])C(=O)NC[C@@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 15, 15, 15, 15, 27, 34, 34, 29, 34, 34, 15, 15, 15, 15, 15, 15, 15, 3, 3, 3, 3, 5, 5, 5, 3, 2, 2, 1, 5, 5, 15, 15, 27, 27, 34, 34, 34, 34, 34, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 3, 3, 6] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 40] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 549) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/549 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/549' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)NC[C@@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O) `ZINC001219726421.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001219726421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001219726421 none COc1cc(C[C@]([O-])([SiH3])C(=O)NC[C@@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 3, 3, 3, 2, 1, 1, 1, 1, 1, 1, 1, 11, 22, 22, 22, 22, 34, 37, 37, 35, 37, 37, 22, 22, 22, 22, 22, 22, 22, 3, 3, 3, 3, 6, 6, 6, 3, 2, 2, 1, 7, 7, 22, 22, 34, 34, 37, 37, 37, 37, 37, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 3, 3, 6] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 40] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001219726421 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421 Building ZINC001219726421 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001219726421 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 546) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)NC[C@@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O) `ZINC001219726421.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001219726421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001219726421 none COc1cc(C[C@@]([O-])([SiH3])C(=O)NC[C@@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 15, 15, 15, 15, 27, 34, 34, 29, 34, 34, 15, 15, 15, 15, 15, 15, 15, 3, 3, 3, 3, 5, 5, 5, 3, 2, 2, 1, 5, 5, 15, 15, 27, 27, 34, 34, 34, 34, 34, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 3, 3, 6] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 40] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 547) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)NC[C@@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O) `ZINC001219726421.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001219726421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001219726421 none COc1cc(C[C@]([O-])([SiH3])C(=O)NC[C@@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 3, 3, 3, 2, 1, 1, 1, 1, 1, 1, 1, 11, 22, 22, 22, 22, 34, 37, 37, 35, 37, 37, 22, 22, 22, 22, 22, 22, 22, 3, 3, 3, 3, 6, 6, 6, 3, 2, 2, 1, 7, 7, 22, 22, 34, 34, 37, 37, 37, 37, 37, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 3, 3, 6] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 40] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 548) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/548: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O) `ZINC001219726421.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001219726421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001219726421 none COc1cc(C[C@@]([O-])([SiH3])C(=O)NC[C@@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 15, 15, 15, 15, 27, 34, 34, 29, 34, 34, 15, 15, 15, 15, 15, 15, 15, 3, 3, 3, 3, 5, 5, 5, 3, 2, 2, 1, 5, 5, 15, 15, 27, 27, 34, 34, 34, 34, 34, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 3, 3, 6] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 40] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 549) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/549: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O) `ZINC001219726421.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001219726421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001219726421 none COc1cc(C[C@]([O-])([SiH3])C(=O)NC[C@@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 3, 3, 3, 2, 1, 1, 1, 1, 1, 1, 1, 11, 22, 22, 22, 22, 34, 37, 37, 35, 37, 37, 22, 22, 22, 22, 22, 22, 22, 3, 3, 3, 3, 6, 6, 6, 3, 2, 2, 1, 7, 7, 22, 22, 34, 34, 37, 37, 37, 37, 37, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 3, 3, 6] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 40] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001219726421 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421 Building ZINC001219726421 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001219726421 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 546) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)NC[C@@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O) `ZINC001219726421.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001219726421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001219726421 none COc1cc(C[C@@]([O-])([SiH3])C(=O)NC[C@@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 15, 15, 15, 15, 27, 34, 34, 29, 34, 34, 15, 15, 15, 15, 15, 15, 15, 3, 3, 3, 3, 5, 5, 5, 3, 2, 2, 1, 5, 5, 15, 15, 27, 27, 34, 34, 34, 34, 34, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 3, 3, 6] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 40] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 547) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)NC[C@@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O) `ZINC001219726421.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001219726421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001219726421 none COc1cc(C[C@]([O-])([SiH3])C(=O)NC[C@@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 3, 3, 3, 2, 1, 1, 1, 1, 1, 1, 1, 11, 22, 22, 22, 22, 34, 37, 37, 35, 37, 37, 22, 22, 22, 22, 22, 22, 22, 3, 3, 3, 3, 6, 6, 6, 3, 2, 2, 1, 7, 7, 22, 22, 34, 34, 37, 37, 37, 37, 37, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 3, 3, 6] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 40] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 548) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/548: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O) `ZINC001219726421.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001219726421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001219726421 none COc1cc(C[C@@]([O-])([SiH3])C(=O)NC[C@@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 15, 15, 15, 15, 27, 34, 34, 29, 34, 34, 15, 15, 15, 15, 15, 15, 15, 3, 3, 3, 3, 5, 5, 5, 3, 2, 2, 1, 5, 5, 15, 15, 27, 27, 34, 34, 34, 34, 34, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 3, 3, 6] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 40] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 549) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/549: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O) `ZINC001219726421.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001219726421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001219726421 none COc1cc(C[C@]([O-])([SiH3])C(=O)NC[C@@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 3, 3, 3, 2, 1, 1, 1, 1, 1, 1, 1, 11, 22, 22, 22, 22, 34, 37, 37, 35, 37, 37, 22, 22, 22, 22, 22, 22, 22, 3, 3, 3, 3, 6, 6, 6, 3, 2, 2, 1, 7, 7, 22, 22, 34, 34, 37, 37, 37, 37, 37, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 3, 3, 6] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 40] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001219726421 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421 Building ZINC001219726421 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001219726421 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 546) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)NC[C@@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O) `ZINC001219726421.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001219726421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001219726421 none COc1cc(C[C@@]([O-])([SiH3])C(=O)NC[C@@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 15, 15, 15, 15, 27, 34, 34, 29, 34, 34, 15, 15, 15, 15, 15, 15, 15, 3, 3, 3, 3, 5, 5, 5, 3, 2, 2, 1, 5, 5, 15, 15, 27, 27, 34, 34, 34, 34, 34, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 3, 3, 6] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 40] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 547) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)NC[C@@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O) `ZINC001219726421.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001219726421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001219726421 none COc1cc(C[C@]([O-])([SiH3])C(=O)NC[C@@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 3, 3, 3, 2, 1, 1, 1, 1, 1, 1, 1, 11, 22, 22, 22, 22, 34, 37, 37, 35, 37, 37, 22, 22, 22, 22, 22, 22, 22, 3, 3, 3, 3, 6, 6, 6, 3, 2, 2, 1, 7, 7, 22, 22, 34, 34, 37, 37, 37, 37, 37, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 3, 3, 6] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 40] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 548) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/548: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O) `ZINC001219726421.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001219726421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001219726421 none COc1cc(C[C@@]([O-])([SiH3])C(=O)NC[C@@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 15, 15, 15, 15, 27, 34, 34, 29, 34, 34, 15, 15, 15, 15, 15, 15, 15, 3, 3, 3, 3, 5, 5, 5, 3, 2, 2, 1, 5, 5, 15, 15, 27, 27, 34, 34, 34, 34, 34, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 3, 3, 6] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 40] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 549) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/549: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O) `ZINC001219726421.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001219726421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001219726421 none COc1cc(C[C@]([O-])([SiH3])C(=O)NC[C@@H]2CN(Cc3ccccc3)CC23CCNCC3)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 3, 3, 3, 2, 1, 1, 1, 1, 1, 1, 1, 11, 22, 22, 22, 22, 34, 37, 37, 35, 37, 37, 22, 22, 22, 22, 22, 22, 22, 3, 3, 3, 3, 6, 6, 6, 3, 2, 2, 1, 7, 7, 22, 22, 34, 34, 37, 37, 37, 37, 37, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 3, 3, 6] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 40] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001219726421 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001219726421 Building ZINC001221352892 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001221352892' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001221352892 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001221352892 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001221352892/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001221352892 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 550) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/550 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/550' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)Nc2ccc3c(C)cc(=O)oc3c2)ccc1O) `ZINC001221352892.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001221352892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001221352892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001221352892 none COc1cc(C[C@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)Nc2ccc3c(C)cc(=O)oc3c2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'O.3', '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, 5, 5, 5, 5, 5, 7, 10, 1, 11, 8, 1, 1, 1, 1, 1, 5, 1, 1, 11, 12, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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, 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, 6, 8, 9, 8, 18, 18, 18, 22, 22, 22, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 5, 5, 5, 5, 8, 8, 8, 5, 3, 3, 2, 6, 6, 9, 9, 9, 9, 9, 9, 18, 18, 22, 37, 37, 37, 37, 37, 37, 37, 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, 60, 61, 62, 63, 64]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001221352892 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001221352892/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001221352892 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 551) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/551 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/551' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)Nc2ccc3c(C)cc(=O)oc3c2)ccc1O) `ZINC001221352892.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001221352892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001221352892/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001221352892 none COc1cc(C[C@@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)Nc2ccc3c(C)cc(=O)oc3c2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'O.3', '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, 5, 5, 5, 5, 5, 7, 10, 1, 11, 8, 1, 1, 1, 1, 1, 5, 1, 1, 11, 12, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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, 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, 3, 3, 3, 2, 1, 1, 1, 1, 1, 1, 1, 7, 8, 9, 8, 17, 17, 17, 22, 22, 22, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 3, 3, 3, 3, 6, 6, 6, 3, 2, 2, 1, 7, 7, 9, 9, 9, 9, 9, 9, 17, 17, 22, 35, 35, 35, 35, 35, 35, 35, 3, 3, 6] 100 rigid atoms, others: [43, 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, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001221352892 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001221352892 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001221352892/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001221352892/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001221352892 Building ZINC001221352892 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001221352892' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001221352892 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001221352892 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001221352892/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001221352892 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 550) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)Nc2ccc3c(C)cc(=O)oc3c2)ccc1O) `ZINC001221352892.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001221352892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001221352892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001221352892 none COc1cc(C[C@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)Nc2ccc3c(C)cc(=O)oc3c2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'O.3', '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, 5, 5, 5, 5, 5, 7, 10, 1, 11, 8, 1, 1, 1, 1, 1, 5, 1, 1, 11, 12, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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, 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, 6, 8, 9, 8, 18, 18, 18, 22, 22, 22, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 5, 5, 5, 5, 8, 8, 8, 5, 3, 3, 2, 6, 6, 9, 9, 9, 9, 9, 9, 18, 18, 22, 37, 37, 37, 37, 37, 37, 37, 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, 60, 61, 62, 63, 64]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001221352892 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001221352892/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001221352892 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 551) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc(C[C@@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)Nc2ccc3c(C)cc(=O)oc3c2)ccc1O) `ZINC001221352892.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001221352892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001221352892/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001221352892 none COc1cc(C[C@@]([O-])([SiH3])C(=O)NCCCC[C@H](N)C(=O)Nc2ccc3c(C)cc(=O)oc3c2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'O.3', '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, 5, 5, 5, 5, 5, 7, 10, 1, 11, 8, 1, 1, 1, 1, 1, 5, 1, 1, 11, 12, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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, 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, 3, 3, 3, 2, 1, 1, 1, 1, 1, 1, 1, 7, 8, 9, 8, 17, 17, 17, 22, 22, 22, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 3, 3, 3, 3, 6, 6, 6, 3, 2, 2, 1, 7, 7, 9, 9, 9, 9, 9, 9, 17, 17, 22, 35, 35, 35, 35, 35, 35, 35, 3, 3, 6] 100 rigid atoms, others: [43, 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, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001221352892 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001221352892 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001221352892/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001221352892/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001221352892 Building ZINC001303384141 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384141' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384141 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001303384141 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384141/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384141 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 552) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/552 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/552' -> `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[C@@H](C(=O)N[C@H]2CCC[C@H](O)C2)C1) `ZINC001303384141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001303384141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001303384141 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(=O)N[C@H]2CCC[C@H](O)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', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 7, 7, 2, 7, 7, 2, 2, 1, 1, 1, 2, 3, 4, 4, 4, 4, 4, 4, 4, 10, 10, 12, 35, 35, 35, 35, 35, 35, 35, 35, 4, 2, 2, 2, 7, 7, 2, 7, 7, 2, 2, 2, 4, 4, 4, 4, 4, 4, 10, 35, 35, 35, 35, 35, 35, 105, 35, 35, 4, 4] 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, 64]) total number of confs: 214 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384141 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384141/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384141 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 553) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/553 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/553' -> `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[C@@H](C(=O)N[C@H]2CCC[C@H](O)C2)C1) `ZINC001303384141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001303384141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001303384141 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(=O)N[C@H]2CCC[C@H](O)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', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 4, 5, 5, 2, 2, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 41, 41, 41, 41, 41, 41, 41, 41, 3, 2, 2, 2, 5, 5, 5, 5, 5, 2, 2, 2, 3, 3, 3, 3, 3, 3, 14, 41, 41, 41, 41, 41, 41, 123, 41, 41, 3, 3] 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, 64]) total number of confs: 250 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384141 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001303384141 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384141/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384141/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384141 Building ZINC001303384141 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384141' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384141 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001303384141 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384141/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384141 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 552) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(=O)N[C@H]2CCC[C@H](O)C2)C1) `ZINC001303384141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001303384141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001303384141 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(=O)N[C@H]2CCC[C@H](O)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', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 7, 7, 2, 7, 7, 2, 2, 1, 1, 1, 2, 3, 4, 4, 4, 4, 4, 4, 4, 10, 10, 12, 35, 35, 35, 35, 35, 35, 35, 35, 4, 2, 2, 2, 7, 7, 2, 7, 7, 2, 2, 2, 4, 4, 4, 4, 4, 4, 10, 35, 35, 35, 35, 35, 35, 105, 35, 35, 4, 4] 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, 64]) total number of confs: 214 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384141 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384141/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384141 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 553) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(=O)N[C@H]2CCC[C@H](O)C2)C1) `ZINC001303384141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001303384141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001303384141 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(=O)N[C@H]2CCC[C@H](O)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', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 4, 5, 5, 2, 2, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 41, 41, 41, 41, 41, 41, 41, 41, 3, 2, 2, 2, 5, 5, 5, 5, 5, 2, 2, 2, 3, 3, 3, 3, 3, 3, 14, 41, 41, 41, 41, 41, 41, 123, 41, 41, 3, 3] 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, 64]) total number of confs: 250 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384141 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001303384141 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384141/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384141/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384141 Building ZINC001303384143 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384143' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384143 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001303384143 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384143/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384143 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 554) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/554 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/554' -> `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[C@@H](C(=O)N[C@@H]2CCC[C@H](O)C2)C1) `ZINC001303384143.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001303384143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001303384143 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(=O)N[C@@H]2CCC[C@H](O)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', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 7, 7, 4, 7, 7, 2, 2, 1, 1, 1, 2, 3, 4, 4, 4, 4, 4, 4, 4, 15, 15, 24, 35, 35, 35, 35, 35, 35, 35, 35, 4, 2, 2, 2, 7, 7, 7, 7, 7, 2, 2, 2, 4, 4, 4, 4, 4, 4, 15, 35, 35, 35, 35, 35, 35, 105, 35, 35, 4, 4] 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, 64]) total number of confs: 220 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384143 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384143/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384143 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 555) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/555 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/555' -> `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[C@@H](C(=O)N[C@@H]2CCC[C@H](O)C2)C1) `ZINC001303384143.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001303384143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384143/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001303384143 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(=O)N[C@@H]2CCC[C@H](O)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', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 6, 6, 2, 6, 6, 2, 2, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 27, 36, 36, 36, 36, 36, 36, 36, 36, 4, 2, 2, 2, 6, 6, 2, 6, 6, 2, 2, 2, 4, 4, 4, 4, 4, 4, 16, 36, 36, 36, 36, 36, 36, 108, 36, 36, 4, 4] 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, 64]) total number of confs: 219 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384143 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001303384143 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384143/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384143/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384143 Building ZINC001303384143 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384143' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384143 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001303384143 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384143/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384143 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 554) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(=O)N[C@@H]2CCC[C@H](O)C2)C1) `ZINC001303384143.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001303384143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001303384143 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(=O)N[C@@H]2CCC[C@H](O)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', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 7, 7, 4, 7, 7, 2, 2, 1, 1, 1, 2, 3, 4, 4, 4, 4, 4, 4, 4, 15, 15, 24, 35, 35, 35, 35, 35, 35, 35, 35, 4, 2, 2, 2, 7, 7, 7, 7, 7, 2, 2, 2, 4, 4, 4, 4, 4, 4, 15, 35, 35, 35, 35, 35, 35, 105, 35, 35, 4, 4] 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, 64]) total number of confs: 220 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384143 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384143/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384143 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 555) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(=O)N[C@@H]2CCC[C@H](O)C2)C1) `ZINC001303384143.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001303384143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384143/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001303384143 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(=O)N[C@@H]2CCC[C@H](O)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', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 6, 6, 2, 6, 6, 2, 2, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 27, 36, 36, 36, 36, 36, 36, 36, 36, 4, 2, 2, 2, 6, 6, 2, 6, 6, 2, 2, 2, 4, 4, 4, 4, 4, 4, 16, 36, 36, 36, 36, 36, 36, 108, 36, 36, 4, 4] 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, 64]) total number of confs: 219 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384143 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001303384143 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384143/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384143/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384143 Building ZINC001303384145 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384145' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384145 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001303384145 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384145/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384145 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 556) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/556 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/556' -> `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[C@@H](C(=O)N[C@@H]2CCC[C@@H](O)C2)C1) `ZINC001303384145.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001303384145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001303384145 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(=O)N[C@@H]2CCC[C@@H](O)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', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 2, 2, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 16, 33, 33, 33, 33, 33, 33, 33, 33, 3, 2, 2, 2, 8, 8, 2, 8, 8, 2, 2, 2, 3, 3, 3, 3, 3, 3, 11, 33, 33, 33, 33, 33, 33, 99, 33, 33, 3, 3] 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, 64]) total number of confs: 211 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384145 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384145/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384145 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 557) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/557 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/557' -> `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[C@@H](C(=O)N[C@@H]2CCC[C@@H](O)C2)C1) `ZINC001303384145.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001303384145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384145/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001303384145 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(=O)N[C@@H]2CCC[C@@H](O)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', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 24, 43, 43, 43, 43, 43, 43, 43, 43, 4, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 4, 4, 4, 4, 4, 4, 16, 43, 43, 43, 43, 43, 43, 129, 43, 43, 4, 4] 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, 64]) total number of confs: 268 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384145 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001303384145 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384145/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384145/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384145 Building ZINC001303384145 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384145' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384145 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001303384145 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384145/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384145 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 556) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/556: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(=O)N[C@@H]2CCC[C@@H](O)C2)C1) `ZINC001303384145.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001303384145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001303384145 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(=O)N[C@@H]2CCC[C@@H](O)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', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 2, 2, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 16, 33, 33, 33, 33, 33, 33, 33, 33, 3, 2, 2, 2, 8, 8, 2, 8, 8, 2, 2, 2, 3, 3, 3, 3, 3, 3, 11, 33, 33, 33, 33, 33, 33, 99, 33, 33, 3, 3] 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, 64]) total number of confs: 211 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384145 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384145/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384145 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 557) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/557: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(=O)N[C@@H]2CCC[C@@H](O)C2)C1) `ZINC001303384145.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001303384145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384145/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001303384145 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(=O)N[C@@H]2CCC[C@@H](O)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', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 24, 43, 43, 43, 43, 43, 43, 43, 43, 4, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 4, 4, 4, 4, 4, 4, 16, 43, 43, 43, 43, 43, 43, 129, 43, 43, 4, 4] 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, 64]) total number of confs: 268 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384145 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001303384145 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384145/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384145/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384145 Building ZINC001303384147 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384147' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384147 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001303384147 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384147/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384147 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 558) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/558 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/558' -> `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[C@@H](C(=O)N[C@H]2CCC[C@@H](O)C2)C1) `ZINC001303384147.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001303384147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001303384147 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(=O)N[C@H]2CCC[C@@H](O)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', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 6, 6, 2, 6, 6, 2, 2, 1, 1, 1, 2, 3, 4, 4, 4, 4, 4, 4, 4, 14, 14, 20, 36, 36, 36, 36, 36, 36, 36, 36, 4, 2, 2, 2, 6, 6, 2, 6, 6, 2, 2, 2, 4, 4, 4, 4, 4, 4, 14, 36, 36, 36, 36, 36, 36, 108, 36, 36, 4, 4] 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, 64]) total number of confs: 221 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384147 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384147/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384147 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 559) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/559 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/559' -> `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[C@@H](C(=O)N[C@H]2CCC[C@@H](O)C2)C1) `ZINC001303384147.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001303384147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384147/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001303384147 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(=O)N[C@H]2CCC[C@@H](O)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', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 6, 6, 3, 6, 6, 2, 2, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 22, 38, 38, 38, 38, 38, 38, 38, 38, 4, 2, 2, 2, 6, 6, 3, 6, 6, 2, 2, 2, 4, 4, 4, 4, 4, 4, 16, 38, 38, 38, 38, 38, 38, 114, 38, 38, 4, 4] 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, 64]) total number of confs: 238 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384147 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001303384147 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384147/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384147/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384147 Building ZINC001303384147 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384147' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384147 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001303384147 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384147/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384147 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 558) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(=O)N[C@H]2CCC[C@@H](O)C2)C1) `ZINC001303384147.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001303384147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001303384147 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(=O)N[C@H]2CCC[C@@H](O)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', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 6, 6, 2, 6, 6, 2, 2, 1, 1, 1, 2, 3, 4, 4, 4, 4, 4, 4, 4, 14, 14, 20, 36, 36, 36, 36, 36, 36, 36, 36, 4, 2, 2, 2, 6, 6, 2, 6, 6, 2, 2, 2, 4, 4, 4, 4, 4, 4, 14, 36, 36, 36, 36, 36, 36, 108, 36, 36, 4, 4] 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, 64]) total number of confs: 221 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384147 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384147/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384147 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 559) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(=O)N[C@H]2CCC[C@@H](O)C2)C1) `ZINC001303384147.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001303384147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384147/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001303384147 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(=O)N[C@H]2CCC[C@@H](O)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', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 11, 8, 5, 7, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 6, 6, 3, 6, 6, 2, 2, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 22, 38, 38, 38, 38, 38, 38, 38, 38, 4, 2, 2, 2, 6, 6, 3, 6, 6, 2, 2, 2, 4, 4, 4, 4, 4, 4, 16, 38, 38, 38, 38, 38, 38, 114, 38, 38, 4, 4] 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, 64]) total number of confs: 238 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384147 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001303384147 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384147/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384147/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001303384147 Building ZINC001304117541 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001304117541' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001304117541 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001304117541 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001304117541/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001304117541 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 560) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/560 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/560' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nnc(NS(=O)(=O)c2cccc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)c2)n1) `ZINC001304117541.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001304117541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001304117541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001304117541 none Cn1nnc(NS(=O)(=O)c2cccc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 46, 37, 25, 15, 25, 25, 15, 15, 15, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 15, 46, 46, 46, 46, 37, 15, 15, 15, 3, 3, 1, 3, 15] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001304117541 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001304117541/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001304117541 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 561) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/561 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/561' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nnc(NS(=O)(=O)c2cccc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)c2)n1) `ZINC001304117541.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001304117541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001304117541/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001304117541 none Cn1nnc(NS(=O)(=O)c2cccc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 37, 24, 15, 24, 24, 15, 15, 15, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 15, 45, 45, 45, 45, 37, 15, 15, 15, 3, 3, 1, 3, 15] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001304117541 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001304117541 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001304117541/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001304117541/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001304117541 Building ZINC001304117541 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001304117541' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001304117541 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001304117541 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001304117541/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001304117541 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 560) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1nnc(NS(=O)(=O)c2cccc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)c2)n1) `ZINC001304117541.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001304117541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001304117541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001304117541 none Cn1nnc(NS(=O)(=O)c2cccc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 46, 37, 25, 15, 25, 25, 15, 15, 15, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 15, 46, 46, 46, 46, 37, 15, 15, 15, 3, 3, 1, 3, 15] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001304117541 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001304117541/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001304117541 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 561) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1nnc(NS(=O)(=O)c2cccc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)c2)n1) `ZINC001304117541.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001304117541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001304117541/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001304117541 none Cn1nnc(NS(=O)(=O)c2cccc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 37, 24, 15, 24, 24, 15, 15, 15, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 15, 45, 45, 45, 45, 37, 15, 15, 15, 3, 3, 1, 3, 15] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001304117541 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001304117541 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001304117541/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001304117541/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001304117541 Building ZINC001304241616 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001304241616' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001304241616 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001304241616 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001304241616/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001304241616 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 562) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/562 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/562' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)COc1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)ccc1Br) `ZINC001304241616.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001304241616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001304241616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001304241616 none CC(C)COc1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', '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, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 28, 30, 24, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 8, 8, 8, 8, 30, 30, 30, 30, 30, 30, 30, 28, 28, 8, 2, 1, 4, 4, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [43, 38, 9, 42, 11, 12, 13, 14, 15, 16, 20, 21, 22, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 45, 46]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001304241616 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001304241616/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001304241616 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 563) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/563 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/563' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)COc1cc(NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)ccc1Br) `ZINC001304241616.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001304241616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001304241616/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001304241616 none CC(C)COc1cc(NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', '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, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 27, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 8, 8, 8, 8, 30, 30, 30, 30, 30, 30, 30, 29, 29, 8, 2, 1, 4, 4, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [43, 38, 9, 42, 11, 12, 13, 14, 15, 16, 20, 21, 22, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 45, 46]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001304241616 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001304241616 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001304241616/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001304241616/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001304241616 Building ZINC001304241616 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001304241616' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001304241616 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001304241616 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001304241616/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001304241616 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 562) grep: /scratch/xiaobo/418326/xbt-8058088.46/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)COc1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)ccc1Br) `ZINC001304241616.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001304241616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001304241616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001304241616 none CC(C)COc1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', '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, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 28, 30, 24, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 8, 8, 8, 8, 30, 30, 30, 30, 30, 30, 30, 28, 28, 8, 2, 1, 4, 4, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [43, 38, 9, 42, 11, 12, 13, 14, 15, 16, 20, 21, 22, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 45, 46]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001304241616 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001304241616/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001304241616 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 563) grep: /scratch/xiaobo/418326/xbt-8058088.46/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)COc1cc(NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)ccc1Br) `ZINC001304241616.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001304241616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001304241616/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001304241616 none CC(C)COc1cc(NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', '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, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 27, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 8, 8, 8, 8, 30, 30, 30, 30, 30, 30, 30, 29, 29, 8, 2, 1, 4, 4, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [43, 38, 9, 42, 11, 12, 13, 14, 15, 16, 20, 21, 22, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 45, 46]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001304241616 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001304241616 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001304241616/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001304241616/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001304241616 Building ZINC001306067828 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306067828' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306067828 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001306067828 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306067828/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306067828 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 564) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/564 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/564' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCN(C(=O)[C@@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC001306067828.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001306067828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306067828/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001306067828 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 17, 22, 17, 17, 17, 14, 2, 6, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 3, 3, 2, 3, 3, 3, 17, 17, 29, 29, 29, 29, 29, 29, 29, 29, 29, 17, 17, 17, 17, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 17, 17, 17, 17] 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, 62, 63, 64, 65]) total number of confs: 70 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306067828 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306067828/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306067828 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 565) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/565 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/565' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCN(C(=O)[C@@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC001306067828.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001306067828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306067828/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001306067828 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 29, 28, 28, 28, 24, 4, 11, 4, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 6, 6, 4, 6, 6, 6, 28, 28, 29, 29, 29, 29, 29, 29, 29, 29, 29, 28, 28, 28, 28, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 28, 28, 28, 28] 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, 62, 63, 64, 65]) total number of confs: 72 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306067828 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001306067828 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306067828/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306067828/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306067828 Building ZINC001306067828 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306067828' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306067828 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001306067828 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306067828/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306067828 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 564) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC(C)(C)OC(=O)N1CCN(C(=O)[C@@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC001306067828.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001306067828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306067828/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001306067828 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 17, 22, 17, 17, 17, 14, 2, 6, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 3, 3, 2, 3, 3, 3, 17, 17, 29, 29, 29, 29, 29, 29, 29, 29, 29, 17, 17, 17, 17, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 17, 17, 17, 17] 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, 62, 63, 64, 65]) total number of confs: 70 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306067828 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306067828/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306067828 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 565) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC(C)(C)OC(=O)N1CCN(C(=O)[C@@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC001306067828.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001306067828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306067828/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001306067828 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 29, 28, 28, 28, 24, 4, 11, 4, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 6, 6, 4, 6, 6, 6, 28, 28, 29, 29, 29, 29, 29, 29, 29, 29, 29, 28, 28, 28, 28, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 28, 28, 28, 28] 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, 62, 63, 64, 65]) total number of confs: 72 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306067828 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001306067828 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306067828/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306067828/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306067828 Building ZINC001306586357 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306586357' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306586357 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001306586357 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306586357/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306586357 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 566) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/566 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/566' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)CC(=O)N1CCOCC1) `ZINC001306586357.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001306586357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306586357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001306586357 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)CC(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 2, 2, 3, 3, 6, 9, 9, 19, 19, 19, 19, 19, 2, 2, 2, 16, 16, 2, 16, 2, 2, 2, 3, 3, 3, 6, 6, 19, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 85 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306586357 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306586357/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306586357 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 567) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/567 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/567' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)CC(=O)N1CCOCC1) `ZINC001306586357.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001306586357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306586357/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001306586357 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)CC(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 2, 2, 3, 3, 6, 11, 11, 19, 19, 19, 19, 19, 2, 2, 2, 16, 16, 3, 16, 2, 2, 2, 3, 3, 3, 6, 6, 19, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 93 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306586357 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001306586357 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306586357/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306586357/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306586357 Building ZINC001306586357 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306586357' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306586357 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001306586357 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306586357/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306586357 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 566) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)CC(=O)N1CCOCC1) `ZINC001306586357.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001306586357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306586357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001306586357 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)CC(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 2, 2, 3, 3, 6, 9, 9, 19, 19, 19, 19, 19, 2, 2, 2, 16, 16, 2, 16, 2, 2, 2, 3, 3, 3, 6, 6, 19, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 85 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306586357 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306586357/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306586357 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 567) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)CC(=O)N1CCOCC1) `ZINC001306586357.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001306586357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306586357/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001306586357 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)CC(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 2, 2, 3, 3, 6, 11, 11, 19, 19, 19, 19, 19, 2, 2, 2, 16, 16, 3, 16, 2, 2, 2, 3, 3, 3, 6, 6, 19, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 93 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306586357 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001306586357 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306586357/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306586357/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306586357 Building ZINC001306870281 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306870281' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306870281 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001306870281 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306870281/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306870281 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 568) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/568 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/568' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H](C)O1) `ZINC001306870281.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001306870281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306870281/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001306870281 none COC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H](C)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 9, 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] 0 hydrogens 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, 4, 9, 4, 4, 4, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 4, 4, 4, 4, 4, 9, 9, 9, 4, 4, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 4, 4, 4, 4, 4] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306870281 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306870281/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306870281 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 569) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/569 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/569' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H](C)O1) `ZINC001306870281.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001306870281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306870281/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001306870281 none COC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H](C)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 9, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 3, 7, 3, 3, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 3, 3, 3, 3, 3, 7, 7, 7, 3, 3, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 3, 3, 3, 3, 3] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306870281 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001306870281 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306870281/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306870281/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306870281 Building ZINC001306870281 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306870281' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306870281 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001306870281 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306870281/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306870281 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 568) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H](C)O1) `ZINC001306870281.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001306870281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306870281/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001306870281 none COC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H](C)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 9, 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] 0 hydrogens 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, 4, 9, 4, 4, 4, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 4, 4, 4, 4, 4, 9, 9, 9, 4, 4, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 4, 4, 4, 4, 4] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306870281 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306870281/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306870281 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 569) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H](C)O1) `ZINC001306870281.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001306870281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306870281/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001306870281 none COC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H](C)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 9, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 3, 7, 3, 3, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 3, 3, 3, 3, 3, 7, 7, 7, 3, 3, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 3, 3, 3, 3, 3] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306870281 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001306870281 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306870281/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306870281/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306870281 Building ZINC001306893437 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306893437' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306893437 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001306893437 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306893437/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306893437 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 570) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/570 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/570' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN([S@](C)(=N)=O)CC1) `ZINC001306893437.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001306893437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306893437/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001306893437 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN([S@](C)(=N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o', 'C.3', 'N.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 5, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] 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, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 3, 5, 7, 7, 7, 7, 11, 11, 11, 7, 7, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 7, 7, 7, 7, 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]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306893437 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306893437/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306893437 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 571) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/571 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/571' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN([S@](C)(=N)=O)CC1) `ZINC001306893437.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001306893437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306893437/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001306893437 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN([S@](C)(=N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o', 'C.3', 'N.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 5, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] 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, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 11, 11, 2, 11, 11, 11, 11, 11, 11, 2, 2, 1, 1, 1, 1, 3, 5, 7, 7, 7, 7, 15, 15, 15, 7, 7, 2, 2, 2, 11, 11, 3, 11, 2, 2, 2, 7, 7, 7, 7, 15, 15, 15, 15, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 77 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306893437 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001306893437 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306893437/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306893437/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306893437 Building ZINC001306893437 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306893437' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306893437 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001306893437 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306893437/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306893437 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 570) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/570: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN([S@](C)(=N)=O)CC1) `ZINC001306893437.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001306893437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306893437/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001306893437 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN([S@](C)(=N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o', 'C.3', 'N.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 5, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] 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, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 3, 5, 7, 7, 7, 7, 11, 11, 11, 7, 7, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 7, 7, 7, 7, 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]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306893437 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306893437/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306893437 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 571) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/571: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN([S@](C)(=N)=O)CC1) `ZINC001306893437.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001306893437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306893437/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001306893437 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN([S@](C)(=N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o', 'C.3', 'N.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 5, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] 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, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 11, 11, 2, 11, 11, 11, 11, 11, 11, 2, 2, 1, 1, 1, 1, 3, 5, 7, 7, 7, 7, 15, 15, 15, 7, 7, 2, 2, 2, 11, 11, 3, 11, 2, 2, 2, 7, 7, 7, 7, 15, 15, 15, 15, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 77 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306893437 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001306893437 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306893437/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306893437/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306893437 Building ZINC001306893438 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306893438' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306893438 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001306893438 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306893438/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306893438 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 572) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/572 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/572' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN([S@@](C)(=N)=O)CC1) `ZINC001306893438.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001306893438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306893438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001306893438 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN([S@@](C)(=N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o', 'C.3', 'N.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 5, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] 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, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 14, 14, 2, 14, 14, 14, 14, 14, 14, 2, 2, 1, 1, 1, 1, 3, 5, 7, 7, 7, 7, 13, 13, 13, 7, 7, 2, 2, 2, 14, 14, 8, 14, 2, 2, 2, 7, 7, 7, 7, 13, 13, 13, 13, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 83 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306893438 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306893438/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306893438 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 573) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/573 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/573' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN([S@@](C)(=N)=O)CC1) `ZINC001306893438.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001306893438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306893438/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001306893438 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN([S@@](C)(=N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o', 'C.3', 'N.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 5, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] 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, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 1, 1, 1, 1, 3, 5, 7, 7, 7, 7, 14, 14, 14, 7, 7, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 7, 7, 7, 7, 14, 14, 14, 14, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 74 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306893438 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001306893438 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306893438/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306893438/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306893438 Building ZINC001306893438 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306893438' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306893438 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001306893438 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306893438/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306893438 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 572) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/572: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN([S@@](C)(=N)=O)CC1) `ZINC001306893438.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001306893438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306893438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001306893438 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN([S@@](C)(=N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o', 'C.3', 'N.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 5, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] 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, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 14, 14, 2, 14, 14, 14, 14, 14, 14, 2, 2, 1, 1, 1, 1, 3, 5, 7, 7, 7, 7, 13, 13, 13, 7, 7, 2, 2, 2, 14, 14, 8, 14, 2, 2, 2, 7, 7, 7, 7, 13, 13, 13, 13, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 83 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306893438 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306893438/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306893438 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 573) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/573: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN([S@@](C)(=N)=O)CC1) `ZINC001306893438.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001306893438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306893438/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001306893438 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN([S@@](C)(=N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o', 'C.3', 'N.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 5, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] 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, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 1, 1, 1, 1, 3, 5, 7, 7, 7, 7, 14, 14, 14, 7, 7, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 7, 7, 7, 7, 14, 14, 14, 14, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 74 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306893438 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001306893438 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306893438/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306893438/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001306893438 Building ZINC001325130725 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001325130725' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001325130725 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001325130725 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001325130725/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001325130725 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 574) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/574 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/574' -> `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(OCC(N)=O)CC1) `ZINC001325130725.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001325130725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001325130725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001325130725 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(OCC(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 6, 11, 12, 12, 4, 4, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 4, 4, 4, 4, 4, 11, 11, 12, 12, 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]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001325130725 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001325130725/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001325130725 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 575) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/575 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/575' -> `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(OCC(N)=O)CC1) `ZINC001325130725.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001325130725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001325130725/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001325130725 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(OCC(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 7, 15, 15, 15, 4, 4, 2, 2, 2, 9, 9, 3, 9, 2, 2, 2, 4, 4, 4, 4, 4, 15, 15, 15, 15, 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]) total number of confs: 75 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001325130725 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001325130725 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001325130725/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001325130725/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001325130725 Building ZINC001325130725 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001325130725' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001325130725 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001325130725 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001325130725/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001325130725 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 574) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/574: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(OCC(N)=O)CC1) `ZINC001325130725.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001325130725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001325130725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001325130725 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(OCC(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 6, 11, 12, 12, 4, 4, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 4, 4, 4, 4, 4, 11, 11, 12, 12, 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]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001325130725 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001325130725/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001325130725 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 575) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/575: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(OCC(N)=O)CC1) `ZINC001325130725.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001325130725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001325130725/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001325130725 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(OCC(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 7, 15, 15, 15, 4, 4, 2, 2, 2, 9, 9, 3, 9, 2, 2, 2, 4, 4, 4, 4, 4, 15, 15, 15, 15, 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]) total number of confs: 75 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001325130725 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001325130725 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001325130725/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001325130725/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001325130725 Building ZINC001360766522 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001360766522' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001360766522 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360766522 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001360766522/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001360766522 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 576) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/576 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/576' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2F)cc1Cl) `ZINC001360766522.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360766522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001360766522/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001360766522 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2F)cc1Cl NO_LONG_NAME dock atom 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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 1, 15, 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, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 18, 18, 19, 24, 24, 24, 24, 22, 5, 5, 5, 5, 6, 6, 6, 11, 11, 11, 6, 6, 2, 5, 24, 24, 24, 24, 24, 24, 24, 24, 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, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001360766522 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001360766522/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001360766522 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 577) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/577 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/577' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2F)cc1Cl) `ZINC001360766522.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360766522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001360766522/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001360766522 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2F)cc1Cl NO_LONG_NAME dock atom 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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 1, 15, 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, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 18, 18, 19, 24, 24, 24, 24, 22, 2, 5, 5, 5, 6, 6, 6, 11, 11, 11, 6, 6, 2, 5, 24, 24, 24, 24, 24, 24, 24, 24, 4, 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, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001360766522 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001360766522 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001360766522/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001360766522/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001360766522 Building ZINC001360766522 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001360766522' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001360766522 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001360766522 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001360766522/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001360766522 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 576) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2F)cc1Cl) `ZINC001360766522.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001360766522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001360766522/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001360766522 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2F)cc1Cl NO_LONG_NAME dock atom 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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 1, 15, 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, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 18, 18, 19, 24, 24, 24, 24, 22, 5, 5, 5, 5, 6, 6, 6, 11, 11, 11, 6, 6, 2, 5, 24, 24, 24, 24, 24, 24, 24, 24, 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, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001360766522 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001360766522/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001360766522 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 577) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2F)cc1Cl) `ZINC001360766522.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001360766522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001360766522/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001360766522 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(S(=O)(=O)N3CCOCC3)ccc2F)cc1Cl NO_LONG_NAME dock atom 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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 1, 15, 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, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 18, 18, 19, 24, 24, 24, 24, 22, 2, 5, 5, 5, 6, 6, 6, 11, 11, 11, 6, 6, 2, 5, 24, 24, 24, 24, 24, 24, 24, 24, 4, 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, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001360766522 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001360766522 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001360766522/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001360766522/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001360766522 Building ZINC001361124706 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001361124706' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001361124706 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001361124706 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001361124706/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001361124706 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 578) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/578 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/578' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCCc2ccc(S(=O)(=O)N3CCCCC3)s2)cn1) `ZINC001361124706.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001361124706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001361124706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001361124706 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCCc2ccc(S(=O)(=O)N3CCCCC3)s2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 14, 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, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 9, 9, 5, 5, 1, 1, 1, 1, 4, 4, 4, 9, 9, 13, 13, 13, 13, 30, 30, 30, 42, 42, 42, 42, 35, 13, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 4, 9, 9, 9, 9, 13, 13, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 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, 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/418326/xbt-8058088.46/working/building/ZINC001361124706 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001361124706/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001361124706 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 579) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/579 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/579' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCCc2ccc(S(=O)(=O)N3CCCCC3)s2)cn1) `ZINC001361124706.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001361124706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001361124706/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001361124706 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCCc2ccc(S(=O)(=O)N3CCCCC3)s2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 14, 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, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 7, 7, 4, 4, 1, 1, 1, 1, 4, 4, 4, 9, 9, 13, 13, 13, 13, 32, 32, 33, 43, 43, 43, 43, 38, 13, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 9, 9, 9, 9, 13, 13, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 4] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001361124706 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001361124706 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001361124706/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001361124706/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001361124706 Building ZINC001361124706 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001361124706' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001361124706 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001361124706 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001361124706/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001361124706 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 578) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCCc2ccc(S(=O)(=O)N3CCCCC3)s2)cn1) `ZINC001361124706.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001361124706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001361124706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001361124706 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCCc2ccc(S(=O)(=O)N3CCCCC3)s2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 14, 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, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 9, 9, 5, 5, 1, 1, 1, 1, 4, 4, 4, 9, 9, 13, 13, 13, 13, 30, 30, 30, 42, 42, 42, 42, 35, 13, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 4, 9, 9, 9, 9, 13, 13, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 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, 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/418326/xbt-8058088.46/working/building/ZINC001361124706 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001361124706/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001361124706 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 579) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCCc2ccc(S(=O)(=O)N3CCCCC3)s2)cn1) `ZINC001361124706.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001361124706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001361124706/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001361124706 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCCc2ccc(S(=O)(=O)N3CCCCC3)s2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 14, 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, 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, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 7, 7, 4, 4, 1, 1, 1, 1, 4, 4, 4, 9, 9, 13, 13, 13, 13, 32, 32, 33, 43, 43, 43, 43, 38, 13, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 9, 9, 9, 9, 13, 13, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 4] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001361124706 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001361124706 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001361124706/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001361124706/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001361124706 Building ZINC001436579713 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001436579713' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001436579713 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436579713 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001436579713/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001436579713 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 580) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/580 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/580' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N(CCN2CCOCC2)Cc2sccc2Br)cn1) `ZINC001436579713.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436579713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001436579713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001436579713 none CCn1cc([C@@]([O-])([SiH3])C(=O)N(CCN2CCOCC2)Cc2sccc2Br)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 1, 14, 1, 1, 1, 17, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 3, 8, 11, 17, 17, 17, 17, 17, 3, 4, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 5, 8, 8, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 4, 4, 5, 5, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/418326/xbt-8058088.46/working/building/ZINC001436579713 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001436579713/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001436579713 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 581) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/581 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/581' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N(CCN2CCOCC2)Cc2sccc2Br)cn1) `ZINC001436579713.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436579713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001436579713/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001436579713 none CCn1cc([C@]([O-])([SiH3])C(=O)N(CCN2CCOCC2)Cc2sccc2Br)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 1, 14, 1, 1, 1, 17, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 4, 8, 11, 17, 17, 17, 17, 17, 4, 5, 6, 6, 6, 6, 6, 4, 4, 9, 9, 9, 9, 9, 4, 8, 8, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5, 6, 6, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001436579713 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001436579713 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001436579713/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001436579713/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001436579713 Building ZINC001436579713 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001436579713' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001436579713 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436579713 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001436579713/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001436579713 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 580) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N(CCN2CCOCC2)Cc2sccc2Br)cn1) `ZINC001436579713.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436579713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001436579713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001436579713 none CCn1cc([C@@]([O-])([SiH3])C(=O)N(CCN2CCOCC2)Cc2sccc2Br)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 1, 14, 1, 1, 1, 17, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 3, 8, 11, 17, 17, 17, 17, 17, 3, 4, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 5, 8, 8, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 4, 4, 5, 5, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/418326/xbt-8058088.46/working/building/ZINC001436579713 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001436579713/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001436579713 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 581) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCn1cc([C@]([O-])([SiH3])C(=O)N(CCN2CCOCC2)Cc2sccc2Br)cn1) `ZINC001436579713.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436579713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001436579713/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001436579713 none CCn1cc([C@]([O-])([SiH3])C(=O)N(CCN2CCOCC2)Cc2sccc2Br)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 1, 14, 1, 1, 1, 17, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 4, 8, 11, 17, 17, 17, 17, 17, 4, 5, 6, 6, 6, 6, 6, 4, 4, 9, 9, 9, 9, 9, 4, 8, 8, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5, 6, 6, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001436579713 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001436579713 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001436579713/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001436579713/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001436579713 Building ZINC001436610890 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001436610890' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001436610890 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436610890 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001436610890/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001436610890 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 582) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/582 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/582' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2OCCN2CCN(C(=O)OC(C)(C)C)CC2)cn1) `ZINC001436610890.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436610890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001436610890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001436610890 none Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2OCCN2CCN(C(=O)OC(C)(C)C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 10, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 9, 23, 24, 36, 36, 36, 36, 42, 42, 42, 42, 42, 42, 36, 36, 6, 6, 6, 6, 6, 6, 2, 4, 4, 4, 4, 23, 23, 23, 23, 36, 36, 36, 36, 42, 42, 42, 42, 42, 42, 42, 42, 42, 36, 36, 36, 36, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001436610890 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001436610890/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001436610890 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 583) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/583 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/583' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2OCCN2CCN(C(=O)OC(C)(C)C)CC2)cn1) `ZINC001436610890.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436610890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001436610890/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001436610890 none Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2OCCN2CCN(C(=O)OC(C)(C)C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 10, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 4, 4, 4, 12, 27, 29, 38, 38, 38, 38, 46, 46, 46, 46, 46, 46, 38, 38, 5, 5, 5, 5, 5, 5, 2, 4, 4, 4, 4, 27, 27, 27, 27, 38, 38, 38, 38, 46, 46, 46, 46, 46, 46, 46, 46, 46, 38, 38, 38, 38, 5] 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, 61, 62, 63]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001436610890 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001436610890 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001436610890/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001436610890/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001436610890 Building ZINC001436610890 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001436610890' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001436610890 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436610890 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001436610890/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001436610890 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 582) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2OCCN2CCN(C(=O)OC(C)(C)C)CC2)cn1) `ZINC001436610890.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436610890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001436610890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001436610890 none Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2OCCN2CCN(C(=O)OC(C)(C)C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 10, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 9, 23, 24, 36, 36, 36, 36, 42, 42, 42, 42, 42, 42, 36, 36, 6, 6, 6, 6, 6, 6, 2, 4, 4, 4, 4, 23, 23, 23, 23, 36, 36, 36, 36, 42, 42, 42, 42, 42, 42, 42, 42, 42, 36, 36, 36, 36, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001436610890 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001436610890/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001436610890 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 583) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2OCCN2CCN(C(=O)OC(C)(C)C)CC2)cn1) `ZINC001436610890.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436610890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001436610890/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001436610890 none Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2OCCN2CCN(C(=O)OC(C)(C)C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 10, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 4, 4, 4, 12, 27, 29, 38, 38, 38, 38, 46, 46, 46, 46, 46, 46, 38, 38, 5, 5, 5, 5, 5, 5, 2, 4, 4, 4, 4, 27, 27, 27, 27, 38, 38, 38, 38, 46, 46, 46, 46, 46, 46, 46, 46, 46, 38, 38, 38, 38, 5] 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, 61, 62, 63]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001436610890 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001436610890 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001436610890/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001436610890/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001436610890 Building ZINC001438020750 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001438020750' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001438020750 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438020750 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001438020750/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001438020750 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 584) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/584 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/584' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OC(=O)N2C1CCN(C(=O)OCc2ccccc2)CC1) `ZINC001438020750.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438020750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001438020750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001438020750 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OC(=O)N2C1CCN(C(=O)OCc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 14, 14, 17, 50, 50, 50, 50, 50, 50, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 9, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 41, 42, 43, 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, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001438020750 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001438020750/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001438020750 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 585) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/585 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/585' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OC(=O)N2C1CCN(C(=O)OCc2ccccc2)CC1) `ZINC001438020750.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438020750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001438020750/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001438020750 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OC(=O)N2C1CCN(C(=O)OCc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 15, 15, 19, 50, 50, 50, 50, 50, 50, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 41, 42, 43, 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, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001438020750 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001438020750 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001438020750/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001438020750/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001438020750 Building ZINC001438020750 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001438020750' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001438020750 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438020750 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001438020750/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001438020750 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 584) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OC(=O)N2C1CCN(C(=O)OCc2ccccc2)CC1) `ZINC001438020750.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438020750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001438020750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001438020750 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OC(=O)N2C1CCN(C(=O)OCc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 14, 14, 17, 50, 50, 50, 50, 50, 50, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 9, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 41, 42, 43, 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, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001438020750 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001438020750/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001438020750 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 585) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OC(=O)N2C1CCN(C(=O)OCc2ccccc2)CC1) `ZINC001438020750.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438020750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001438020750/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001438020750 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OC(=O)N2C1CCN(C(=O)OCc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 15, 15, 19, 50, 50, 50, 50, 50, 50, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 41, 42, 43, 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, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001438020750 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001438020750 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001438020750/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001438020750/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001438020750 Building ZINC001438913817 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001438913817' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001438913817 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438913817 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001438913817/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001438913817 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 586) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/586 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/586' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)c1ccc(N2CCN(C(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cc1) `ZINC001438913817.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438913817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001438913817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001438913817 none CNS(=O)(=O)c1ccc(N2CCN(C(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', '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'] dock atom type numbers: [5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 37, 37, 37, 37, 21, 37, 37, 11, 11, 11, 11, 5, 2, 8, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 11, 11, 37, 37, 44, 44, 44, 44, 37, 37, 11, 11, 11, 11, 3, 1, 3, 11, 11, 11, 11, 37, 37] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001438913817 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001438913817/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001438913817 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 587) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/587 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/587' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)c1ccc(N2CCN(C(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cc1) `ZINC001438913817.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438913817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001438913817/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001438913817 none CNS(=O)(=O)c1ccc(N2CCN(C(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', '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'] dock atom type numbers: [5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 39, 32, 39, 39, 25, 39, 39, 13, 13, 13, 13, 6, 2, 9, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 13, 13, 39, 39, 46, 46, 46, 46, 39, 39, 13, 13, 13, 13, 3, 1, 3, 13, 13, 13, 13, 39, 39] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001438913817 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001438913817 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001438913817/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001438913817/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001438913817 Building ZINC001438913817 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001438913817' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001438913817 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438913817 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001438913817/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001438913817 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 586) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CNS(=O)(=O)c1ccc(N2CCN(C(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cc1) `ZINC001438913817.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438913817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001438913817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001438913817 none CNS(=O)(=O)c1ccc(N2CCN(C(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', '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'] dock atom type numbers: [5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 37, 37, 37, 37, 21, 37, 37, 11, 11, 11, 11, 5, 2, 8, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 11, 11, 37, 37, 44, 44, 44, 44, 37, 37, 11, 11, 11, 11, 3, 1, 3, 11, 11, 11, 11, 37, 37] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001438913817 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001438913817/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001438913817 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 587) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CNS(=O)(=O)c1ccc(N2CCN(C(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cc1) `ZINC001438913817.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438913817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001438913817/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001438913817 none CNS(=O)(=O)c1ccc(N2CCN(C(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', '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'] dock atom type numbers: [5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 39, 32, 39, 39, 25, 39, 39, 13, 13, 13, 13, 6, 2, 9, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 13, 13, 39, 39, 46, 46, 46, 46, 39, 39, 13, 13, 13, 13, 3, 1, 3, 13, 13, 13, 13, 39, 39] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001438913817 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001438913817 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001438913817/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001438913817/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001438913817 Building ZINC001439822141 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001439822141' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001439822141 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439822141 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001439822141/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001439822141 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 588) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/588 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/588' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCNC(=O)[C@@H]1c1ccc(I)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001439822141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439822141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001439822141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001439822141 none O=C(N1CCNC(=O)[C@@H]1c1ccc(I)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 1, 1, 1, 1, 18, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 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: [12, 3, 12, 21, 21, 21, 21, 21, 21, 21, 21, 28, 28, 24, 28, 28, 28, 1, 1, 1, 6, 6, 1, 1, 6, 6, 21, 21, 21, 21, 21, 28, 28, 28, 28, 6, 6, 6, 6] 29 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]) total number of confs: 90 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001439822141 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001439822141/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001439822141 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 589) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/589 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/589' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCNC(=O)[C@@H]1c1ccc(I)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001439822141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439822141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001439822141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001439822141 none O=C(N1CCNC(=O)[C@@H]1c1ccc(I)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 1, 1, 1, 1, 18, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [12, 3, 12, 20, 20, 20, 20, 20, 20, 20, 20, 23, 23, 20, 23, 23, 23, 1, 1, 1, 5, 5, 1, 1, 5, 5, 20, 20, 20, 20, 20, 23, 23, 23, 23, 5, 5, 5, 5] 25 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001439822141 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001439822141 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001439822141/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001439822141/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001439822141 Building ZINC001439822141 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001439822141' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001439822141 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439822141 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001439822141/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001439822141 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 588) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: O=C(N1CCNC(=O)[C@@H]1c1ccc(I)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001439822141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439822141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001439822141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001439822141 none O=C(N1CCNC(=O)[C@@H]1c1ccc(I)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 1, 1, 1, 1, 18, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 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: [12, 3, 12, 21, 21, 21, 21, 21, 21, 21, 21, 28, 28, 24, 28, 28, 28, 1, 1, 1, 6, 6, 1, 1, 6, 6, 21, 21, 21, 21, 21, 28, 28, 28, 28, 6, 6, 6, 6] 29 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]) total number of confs: 90 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001439822141 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001439822141/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001439822141 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 589) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: O=C(N1CCNC(=O)[C@@H]1c1ccc(I)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001439822141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439822141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001439822141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001439822141 none O=C(N1CCNC(=O)[C@@H]1c1ccc(I)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 1, 1, 1, 1, 18, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [12, 3, 12, 20, 20, 20, 20, 20, 20, 20, 20, 23, 23, 20, 23, 23, 23, 1, 1, 1, 5, 5, 1, 1, 5, 5, 20, 20, 20, 20, 20, 23, 23, 23, 23, 5, 5, 5, 5] 25 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001439822141 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001439822141 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001439822141/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001439822141/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001439822141 Building ZINC001439822143 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001439822143' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001439822143 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439822143 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001439822143/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001439822143 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 590) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/590 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/590' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCNC(=O)[C@H]1c1ccc(I)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001439822143.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439822143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001439822143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001439822143 none O=C(N1CCNC(=O)[C@H]1c1ccc(I)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 1, 1, 1, 1, 18, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 9, 14, 14, 14, 14, 14, 14, 14, 14, 17, 17, 14, 17, 17, 17, 1, 1, 1, 4, 4, 1, 1, 4, 4, 14, 14, 14, 14, 14, 17, 17, 17, 17, 4, 4, 4, 4] 19 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001439822143 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001439822143/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001439822143 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 591) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/591 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/591' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCNC(=O)[C@H]1c1ccc(I)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001439822143.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439822143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001439822143/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001439822143 none O=C(N1CCNC(=O)[C@H]1c1ccc(I)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 1, 1, 1, 1, 18, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 9, 15, 15, 15, 15, 15, 15, 15, 15, 21, 21, 18, 21, 21, 21, 1, 1, 1, 5, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15, 21, 21, 21, 21, 5, 5, 5, 5] 22 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]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001439822143 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001439822143 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001439822143/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001439822143/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001439822143 Building ZINC001439822143 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001439822143' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001439822143 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439822143 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001439822143/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001439822143 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 590) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: O=C(N1CCNC(=O)[C@H]1c1ccc(I)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001439822143.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439822143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001439822143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001439822143 none O=C(N1CCNC(=O)[C@H]1c1ccc(I)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 1, 1, 1, 1, 18, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 9, 14, 14, 14, 14, 14, 14, 14, 14, 17, 17, 14, 17, 17, 17, 1, 1, 1, 4, 4, 1, 1, 4, 4, 14, 14, 14, 14, 14, 17, 17, 17, 17, 4, 4, 4, 4] 19 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001439822143 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001439822143/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001439822143 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 591) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: O=C(N1CCNC(=O)[C@H]1c1ccc(I)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001439822143.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439822143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001439822143/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001439822143 none O=C(N1CCNC(=O)[C@H]1c1ccc(I)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 1, 1, 1, 1, 18, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 9, 15, 15, 15, 15, 15, 15, 15, 15, 21, 21, 18, 21, 21, 21, 1, 1, 1, 5, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15, 21, 21, 21, 21, 5, 5, 5, 5] 22 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]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001439822143 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001439822143 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001439822143/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001439822143/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001439822143 Building ZINC001440831087 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001440831087' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001440831087 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001440831087 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001440831087/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001440831087 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 592) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/592 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/592' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1)NCc1ccccc1) `ZINC001440831087.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001440831087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001440831087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001440831087 none O=C(CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1)NCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 6, 6, 6, 6, 4, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 20, 20, 40, 41, 41, 40, 41, 41, 14, 14, 6, 6, 6, 6, 3, 3, 6, 6, 6, 6, 20, 40, 40, 41, 41, 40, 41, 41] 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]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001440831087 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001440831087/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001440831087 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 593) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/593 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/593' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1)NCc1ccccc1) `ZINC001440831087.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001440831087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001440831087/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001440831087 none O=C(CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1)NCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 14, 5, 5, 5, 5, 4, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 21, 21, 44, 44, 44, 44, 44, 44, 14, 14, 5, 5, 5, 5, 2, 2, 5, 5, 5, 5, 21, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001440831087 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001440831087 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001440831087/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001440831087/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001440831087 Building ZINC001440831087 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001440831087' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001440831087 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001440831087 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001440831087/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001440831087 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 592) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: O=C(CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1)NCc1ccccc1) `ZINC001440831087.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001440831087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001440831087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001440831087 none O=C(CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1)NCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 6, 6, 6, 6, 4, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 20, 20, 40, 41, 41, 40, 41, 41, 14, 14, 6, 6, 6, 6, 3, 3, 6, 6, 6, 6, 20, 40, 40, 41, 41, 40, 41, 41] 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]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001440831087 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001440831087/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001440831087 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 593) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: O=C(CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1)NCc1ccccc1) `ZINC001440831087.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001440831087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001440831087/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001440831087 none O=C(CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1)NCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 14, 5, 5, 5, 5, 4, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 21, 21, 44, 44, 44, 44, 44, 44, 14, 14, 5, 5, 5, 5, 2, 2, 5, 5, 5, 5, 21, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001440831087 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001440831087 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001440831087/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001440831087/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001440831087 Building ZINC001441119018 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441119018' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441119018 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001441119018 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441119018/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441119018 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 594) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/594 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/594' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C1CCCCC1)S(=O)(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001441119018.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001441119018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441119018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001441119018 none CN(C1CCCCC1)S(=O)(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 5, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 33, 37, 37, 37, 37, 37, 9, 18, 18, 9, 9, 9, 4, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 33, 33, 33, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 9, 9, 9, 9, 5, 5, 5, 5, 9, 9, 9, 9] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441119018 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441119018/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441119018 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 595) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/595 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/595' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C1CCCCC1)S(=O)(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001441119018.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001441119018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441119018/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001441119018 none CN(C1CCCCC1)S(=O)(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 5, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 20, 31, 39, 39, 39, 39, 39, 13, 20, 20, 13, 13, 13, 4, 1, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 31, 31, 31, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 13, 13, 13, 13, 4, 4, 4, 4, 13, 13, 13, 13] 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]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441119018 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001441119018 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441119018/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441119018/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441119018 Building ZINC001441119018 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441119018' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441119018 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001441119018 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441119018/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441119018 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 594) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CN(C1CCCCC1)S(=O)(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001441119018.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001441119018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441119018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001441119018 none CN(C1CCCCC1)S(=O)(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 5, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 33, 37, 37, 37, 37, 37, 9, 18, 18, 9, 9, 9, 4, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 33, 33, 33, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 9, 9, 9, 9, 5, 5, 5, 5, 9, 9, 9, 9] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441119018 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441119018/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441119018 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 595) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CN(C1CCCCC1)S(=O)(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001441119018.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001441119018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441119018/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001441119018 none CN(C1CCCCC1)S(=O)(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 5, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 20, 31, 39, 39, 39, 39, 39, 13, 20, 20, 13, 13, 13, 4, 1, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 31, 31, 31, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 13, 13, 13, 13, 4, 4, 4, 4, 13, 13, 13, 13] 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]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441119018 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001441119018 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441119018/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441119018/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441119018 Building ZINC001441677016 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441677016' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441677016 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001441677016 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441677016/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441677016 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 596) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/596 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/596' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cccc(COCCOc2ccccc2)c1) `ZINC001441677016.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001441677016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441677016/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001441677016 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cccc(COCCOc2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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.3', 'O.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 18, 23, 26, 26, 46, 46, 46, 46, 46, 46, 4, 1, 1, 1, 1, 2, 2, 1, 2, 4, 4, 4, 18, 18, 26, 26, 26, 26, 46, 46, 46, 46, 46, 4] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441677016 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441677016/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441677016 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 597) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/597 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/597' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cccc(COCCOc2ccccc2)c1) `ZINC001441677016.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001441677016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441677016/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001441677016 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cccc(COCCOc2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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.3', 'O.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 4, 4, 18, 22, 22, 22, 43, 43, 43, 43, 43, 43, 4, 1, 1, 1, 1, 2, 2, 1, 2, 4, 4, 4, 18, 18, 22, 22, 22, 22, 43, 43, 43, 43, 43, 4] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 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/418326/xbt-8058088.46/working/building/ZINC001441677016 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001441677016 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441677016/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441677016/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441677016 Building ZINC001441677016 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441677016' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441677016 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001441677016 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441677016/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441677016 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 596) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cccc(COCCOc2ccccc2)c1) `ZINC001441677016.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001441677016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441677016/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001441677016 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cccc(COCCOc2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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.3', 'O.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 18, 23, 26, 26, 46, 46, 46, 46, 46, 46, 4, 1, 1, 1, 1, 2, 2, 1, 2, 4, 4, 4, 18, 18, 26, 26, 26, 26, 46, 46, 46, 46, 46, 4] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441677016 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441677016/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441677016 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 597) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cccc(COCCOc2ccccc2)c1) `ZINC001441677016.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001441677016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441677016/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001441677016 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cccc(COCCOc2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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.3', 'O.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 4, 4, 18, 22, 22, 22, 43, 43, 43, 43, 43, 43, 4, 1, 1, 1, 1, 2, 2, 1, 2, 4, 4, 4, 18, 18, 22, 22, 22, 22, 43, 43, 43, 43, 43, 4] 50 rigid atoms, others: [0, 1, 34, 3, 32, 38, 33, 8, 9, 10, 11, 12, 2, 35, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 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/418326/xbt-8058088.46/working/building/ZINC001441677016 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001441677016 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441677016/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441677016/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441677016 Building ZINC001441953429 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441953429' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441953429 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001441953429 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441953429/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441953429 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 598) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/598 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/598' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H](c1ccc(Br)cc1)C1CCC1) `ZINC001441953429.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001441953429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441953429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001441953429 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H](c1ccc(Br)cc1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 14, 14, 5, 1, 1, 1, 1, 4, 4, 4, 7, 7, 9, 9, 9, 9, 9, 9, 7, 10, 10, 10, 5, 5, 5, 5, 14, 14, 5, 4, 9, 9, 9, 9, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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: 85 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441953429 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441953429/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441953429 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 599) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/599 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/599' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H](c1ccc(Br)cc1)C1CCC1) `ZINC001441953429.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001441953429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441953429/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001441953429 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H](c1ccc(Br)cc1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 13, 13, 13, 5, 1, 1, 1, 1, 4, 4, 4, 7, 7, 11, 11, 11, 11, 11, 11, 9, 14, 14, 14, 5, 5, 5, 5, 13, 13, 5, 4, 11, 11, 11, 11, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441953429 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001441953429 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441953429/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441953429/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441953429 Building ZINC001441953429 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441953429' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441953429 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001441953429 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441953429/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441953429 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 598) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H](c1ccc(Br)cc1)C1CCC1) `ZINC001441953429.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001441953429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441953429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001441953429 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H](c1ccc(Br)cc1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 14, 14, 5, 1, 1, 1, 1, 4, 4, 4, 7, 7, 9, 9, 9, 9, 9, 9, 7, 10, 10, 10, 5, 5, 5, 5, 14, 14, 5, 4, 9, 9, 9, 9, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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: 85 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441953429 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441953429/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441953429 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 599) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H](c1ccc(Br)cc1)C1CCC1) `ZINC001441953429.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001441953429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441953429/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001441953429 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H](c1ccc(Br)cc1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 13, 13, 13, 5, 1, 1, 1, 1, 4, 4, 4, 7, 7, 11, 11, 11, 11, 11, 11, 9, 14, 14, 14, 5, 5, 5, 5, 13, 13, 5, 4, 11, 11, 11, 11, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441953429 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001441953429 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441953429/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441953429/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441953429 Building ZINC001441953451 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441953451' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441953451 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001441953451 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441953451/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441953451 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 600) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/600 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/600' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1ccc(Br)cc1)C1CCC1) `ZINC001441953451.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001441953451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441953451/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001441953451 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1ccc(Br)cc1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 13, 13, 13, 5, 1, 1, 1, 1, 4, 4, 4, 7, 7, 11, 11, 7, 11, 11, 11, 9, 14, 14, 14, 5, 5, 5, 5, 13, 13, 5, 4, 11, 11, 11, 11, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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: 118 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441953451 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441953451/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441953451 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 601) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/601 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/601' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H](c1ccc(Br)cc1)C1CCC1) `ZINC001441953451.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001441953451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441953451/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001441953451 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H](c1ccc(Br)cc1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 14, 14, 5, 1, 1, 1, 1, 4, 4, 4, 7, 7, 9, 9, 9, 9, 9, 9, 8, 11, 11, 11, 5, 5, 5, 5, 14, 14, 5, 4, 9, 9, 9, 9, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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: 86 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441953451 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001441953451 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441953451/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441953451/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441953451 Building ZINC001441953451 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441953451' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441953451 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001441953451 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441953451/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441953451 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 600) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1ccc(Br)cc1)C1CCC1) `ZINC001441953451.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001441953451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441953451/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001441953451 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1ccc(Br)cc1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 13, 13, 13, 5, 1, 1, 1, 1, 4, 4, 4, 7, 7, 11, 11, 7, 11, 11, 11, 9, 14, 14, 14, 5, 5, 5, 5, 13, 13, 5, 4, 11, 11, 11, 11, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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: 118 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441953451 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441953451/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441953451 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 601) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H](c1ccc(Br)cc1)C1CCC1) `ZINC001441953451.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001441953451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441953451/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001441953451 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H](c1ccc(Br)cc1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 14, 14, 5, 1, 1, 1, 1, 4, 4, 4, 7, 7, 9, 9, 9, 9, 9, 9, 8, 11, 11, 11, 5, 5, 5, 5, 14, 14, 5, 4, 9, 9, 9, 9, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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: 86 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441953451 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001441953451 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441953451/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441953451/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001441953451 Building ZINC001443054738 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443054738' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443054738 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001443054738 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443054738/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443054738 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 602) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/602 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/602' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCN(CCOc2ccc(CCNC(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)cc2)CC1) `ZINC001443054738.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001443054738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443054738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001443054738 none CC(=O)N1CCN(CCOc2ccc(CCNC(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 10, 5, 5, 12, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 33, 33, 33, 11, 11, 16, 16, 11, 8, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 16, 16, 11, 11, 8, 8, 3, 2, 2, 2, 2, 2, 2, 16, 16, 50, 50, 50, 50] 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]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443054738 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443054738/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443054738 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 603) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/603 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/603' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCN(CCOc2ccc(CCNC(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)cc2)CC1) `ZINC001443054738.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001443054738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443054738/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001443054738 none CC(=O)N1CCN(CCOc2ccc(CCNC(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 10, 5, 5, 12, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 33, 33, 33, 16, 16, 16, 16, 11, 8, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 16, 16, 11, 11, 8, 8, 3, 2, 2, 2, 2, 2, 2, 16, 16, 50, 50, 50, 50] 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443054738 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001443054738 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443054738/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443054738/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443054738 Building ZINC001443054738 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443054738' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443054738 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001443054738 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443054738/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443054738 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 602) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC(=O)N1CCN(CCOc2ccc(CCNC(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)cc2)CC1) `ZINC001443054738.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001443054738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443054738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001443054738 none CC(=O)N1CCN(CCOc2ccc(CCNC(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 10, 5, 5, 12, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 33, 33, 33, 11, 11, 16, 16, 11, 8, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 16, 16, 11, 11, 8, 8, 3, 2, 2, 2, 2, 2, 2, 16, 16, 50, 50, 50, 50] 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]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443054738 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443054738/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443054738 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 603) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC(=O)N1CCN(CCOc2ccc(CCNC(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)cc2)CC1) `ZINC001443054738.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001443054738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443054738/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001443054738 none CC(=O)N1CCN(CCOc2ccc(CCNC(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 10, 5, 5, 12, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 33, 33, 33, 16, 16, 16, 16, 11, 8, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 16, 16, 11, 11, 8, 8, 3, 2, 2, 2, 2, 2, 2, 16, 16, 50, 50, 50, 50] 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443054738 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001443054738 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443054738/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443054738/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443054738 Building ZINC001443208714 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443208714' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443208714 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001443208714 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443208714/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443208714 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 604) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/604 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/604' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)n(c2ccccc2C(F)(F)F)n1) `ZINC001443208714.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001443208714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443208714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001443208714 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)n(c2ccccc2C(F)(F)F)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.2', '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, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 11, 11, 23, 23, 19, 23, 23, 23, 23, 23, 23, 11, 11, 11, 11, 11, 6, 1, 4, 4, 1, 1, 1, 1, 23, 23, 19, 23] 50 rigid atoms, others: [36, 5, 7, 8, 9, 10, 11, 12, 16, 17, 18, 41, 40, 39, 42] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 43, 44, 45, 46]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443208714 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443208714/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443208714 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 605) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/605 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/605' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)n(c2ccccc2C(F)(F)F)n1) `ZINC001443208714.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001443208714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443208714/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001443208714 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)n(c2ccccc2C(F)(F)F)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.2', '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, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 11, 11, 22, 22, 19, 22, 22, 22, 22, 22, 22, 11, 11, 11, 11, 11, 6, 1, 4, 4, 1, 1, 1, 1, 22, 22, 19, 22] 50 rigid atoms, others: [36, 5, 7, 8, 9, 10, 11, 12, 16, 17, 18, 41, 40, 39, 42] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 43, 44, 45, 46]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443208714 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001443208714 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443208714/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443208714/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443208714 Building ZINC001443208714 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443208714' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443208714 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001443208714 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443208714/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443208714 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 604) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)n(c2ccccc2C(F)(F)F)n1) `ZINC001443208714.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001443208714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443208714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001443208714 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)n(c2ccccc2C(F)(F)F)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.2', '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, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 11, 11, 23, 23, 19, 23, 23, 23, 23, 23, 23, 11, 11, 11, 11, 11, 6, 1, 4, 4, 1, 1, 1, 1, 23, 23, 19, 23] 50 rigid atoms, others: [36, 5, 7, 8, 9, 10, 11, 12, 16, 17, 18, 41, 40, 39, 42] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 43, 44, 45, 46]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443208714 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443208714/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443208714 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 605) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)n(c2ccccc2C(F)(F)F)n1) `ZINC001443208714.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001443208714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443208714/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001443208714 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)n(c2ccccc2C(F)(F)F)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.2', '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, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 11, 11, 22, 22, 19, 22, 22, 22, 22, 22, 22, 11, 11, 11, 11, 11, 6, 1, 4, 4, 1, 1, 1, 1, 22, 22, 19, 22] 50 rigid atoms, others: [36, 5, 7, 8, 9, 10, 11, 12, 16, 17, 18, 41, 40, 39, 42] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 43, 44, 45, 46]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443208714 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001443208714 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443208714/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443208714/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443208714 Building ZINC001443416715 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443416715' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443416715 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001443416715 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443416715/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443416715 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 606) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/606 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/606' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCN(S(=O)(=O)c2cccc3cnccc32)CC1) `ZINC001443416715.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001443416715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443416715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001443416715 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCN(S(=O)(=O)c2cccc3cnccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 4, 5, 8, 8, 8, 8, 8, 16, 16, 16, 36, 36, 36, 36, 36, 36, 36, 36, 36, 8, 8, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 36, 36, 36, 36, 36, 36, 8, 8, 8, 8] 43 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: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443416715 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443416715/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443416715 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 607) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/607 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/607' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCN(S(=O)(=O)c2cccc3cnccc32)CC1) `ZINC001443416715.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001443416715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443416715/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001443416715 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCN(S(=O)(=O)c2cccc3cnccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 2, 3, 4, 7, 7, 7, 7, 7, 16, 16, 16, 42, 42, 42, 42, 42, 42, 42, 42, 42, 7, 7, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 42, 42, 42, 42, 42, 42, 7, 7, 7, 7] 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: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443416715 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001443416715 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443416715/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443416715/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443416715 Building ZINC001443416715 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443416715' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443416715 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001443416715 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443416715/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443416715 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 606) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCN(S(=O)(=O)c2cccc3cnccc32)CC1) `ZINC001443416715.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001443416715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443416715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001443416715 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCN(S(=O)(=O)c2cccc3cnccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 4, 5, 8, 8, 8, 8, 8, 16, 16, 16, 36, 36, 36, 36, 36, 36, 36, 36, 36, 8, 8, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 36, 36, 36, 36, 36, 36, 8, 8, 8, 8] 43 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: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443416715 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443416715/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443416715 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 607) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCN(S(=O)(=O)c2cccc3cnccc32)CC1) `ZINC001443416715.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001443416715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443416715/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001443416715 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCN(S(=O)(=O)c2cccc3cnccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 2, 3, 4, 7, 7, 7, 7, 7, 16, 16, 16, 42, 42, 42, 42, 42, 42, 42, 42, 42, 7, 7, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 42, 42, 42, 42, 42, 42, 7, 7, 7, 7] 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: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443416715 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001443416715 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443416715/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443416715/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443416715 Building ZINC001443668774 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443668774' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443668774 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001443668774 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443668774/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443668774 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 608) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/608 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/608' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H](c1cccnc1)c1ccc(F)c(C)c1) `ZINC001443668774.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001443668774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443668774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001443668774 none CCN(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H](c1cccnc1)c1ccc(F)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', '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.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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 5, 1, 7, 7, 7, 7, 7, 7, 6, 6, 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, 4, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 7, 7, 7, 2, 2, 2, 3, 4, 4, 8, 8, 8, 8, 8, 4, 10, 10, 8, 8, 10, 10, 10, 3, 3, 3, 3, 3, 2, 7, 7, 2, 2, 2, 2, 8, 8, 8, 8, 10, 10, 10, 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, 50, 51, 52, 53, 54]) total number of confs: 62 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443668774 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443668774/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443668774 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 609) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/609 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/609' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H](c1cccnc1)c1ccc(F)c(C)c1) `ZINC001443668774.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001443668774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443668774/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001443668774 none CCN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H](c1cccnc1)c1ccc(F)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', '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.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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 5, 1, 7, 7, 7, 7, 7, 7, 6, 6, 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, 4, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 7, 7, 7, 2, 2, 2, 3, 4, 4, 8, 8, 8, 8, 8, 4, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 3, 3, 2, 7, 7, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 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, 51, 52, 53, 54]) total number of confs: 52 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443668774 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001443668774 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443668774/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443668774/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443668774 Building ZINC001443668774 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443668774' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443668774 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001443668774 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443668774/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443668774 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 608) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCN(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H](c1cccnc1)c1ccc(F)c(C)c1) `ZINC001443668774.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001443668774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443668774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001443668774 none CCN(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H](c1cccnc1)c1ccc(F)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', '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.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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 5, 1, 7, 7, 7, 7, 7, 7, 6, 6, 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, 4, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 7, 7, 7, 2, 2, 2, 3, 4, 4, 8, 8, 8, 8, 8, 4, 10, 10, 8, 8, 10, 10, 10, 3, 3, 3, 3, 3, 2, 7, 7, 2, 2, 2, 2, 8, 8, 8, 8, 10, 10, 10, 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, 50, 51, 52, 53, 54]) total number of confs: 62 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443668774 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443668774/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443668774 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 609) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H](c1cccnc1)c1ccc(F)c(C)c1) `ZINC001443668774.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001443668774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443668774/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001443668774 none CCN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H](c1cccnc1)c1ccc(F)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', '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.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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 5, 1, 7, 7, 7, 7, 7, 7, 6, 6, 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, 4, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 7, 7, 7, 2, 2, 2, 3, 4, 4, 8, 8, 8, 8, 8, 4, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 3, 3, 2, 7, 7, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 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, 51, 52, 53, 54]) total number of confs: 52 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443668774 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001443668774 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443668774/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443668774/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443668774 Building ZINC001443668798 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443668798' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443668798 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001443668798 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443668798/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443668798 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 610) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/610 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/610' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@@H](c1cccnc1)c1ccc(F)c(C)c1) `ZINC001443668798.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001443668798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443668798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001443668798 none CCN(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@@H](c1cccnc1)c1ccc(F)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', '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.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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 5, 1, 7, 7, 7, 7, 7, 7, 6, 6, 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, 4, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 7, 7, 7, 2, 2, 2, 3, 4, 4, 8, 8, 8, 8, 8, 4, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 3, 3, 2, 7, 7, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 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, 51, 52, 53, 54]) total number of confs: 52 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443668798 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443668798/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443668798 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 611) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/611 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/611' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@@H](c1cccnc1)c1ccc(F)c(C)c1) `ZINC001443668798.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001443668798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443668798/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001443668798 none CCN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@@H](c1cccnc1)c1ccc(F)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', '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.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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 5, 1, 7, 7, 7, 7, 7, 7, 6, 6, 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, 4, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 7, 7, 7, 2, 2, 2, 3, 4, 4, 8, 8, 8, 8, 8, 4, 10, 10, 8, 8, 10, 10, 10, 3, 3, 3, 3, 3, 2, 7, 7, 2, 2, 2, 2, 8, 8, 8, 8, 10, 10, 10, 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, 50, 51, 52, 53, 54]) total number of confs: 62 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443668798 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001443668798 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443668798/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443668798/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443668798 Building ZINC001443668798 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443668798' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443668798 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001443668798 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443668798/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443668798 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 610) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCN(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@@H](c1cccnc1)c1ccc(F)c(C)c1) `ZINC001443668798.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001443668798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443668798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001443668798 none CCN(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@@H](c1cccnc1)c1ccc(F)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', '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.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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 5, 1, 7, 7, 7, 7, 7, 7, 6, 6, 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, 4, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 7, 7, 7, 2, 2, 2, 3, 4, 4, 8, 8, 8, 8, 8, 4, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 3, 3, 2, 7, 7, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 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, 51, 52, 53, 54]) total number of confs: 52 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443668798 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443668798/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443668798 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 611) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@@H](c1cccnc1)c1ccc(F)c(C)c1) `ZINC001443668798.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001443668798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443668798/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001443668798 none CCN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@@H](c1cccnc1)c1ccc(F)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', '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.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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 5, 1, 7, 7, 7, 7, 7, 7, 6, 6, 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, 4, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 7, 7, 7, 2, 2, 2, 3, 4, 4, 8, 8, 8, 8, 8, 4, 10, 10, 8, 8, 10, 10, 10, 3, 3, 3, 3, 3, 2, 7, 7, 2, 2, 2, 2, 8, 8, 8, 8, 10, 10, 10, 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, 50, 51, 52, 53, 54]) total number of confs: 62 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443668798 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001443668798 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443668798/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443668798/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001443668798 Building ZINC001444928851 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001444928851 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 612) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/612 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/612' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1)Cc1ccccc1) `ZINC001444928851.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001444928851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001444928851 none CN(CCNC(=O)C1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 31, 25, 5, 5, 4, 5, 4, 4, 4, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 2, 4, 4, 32, 37, 40, 40, 40, 40, 40, 32, 32, 32, 31, 31, 25, 25, 5, 4, 4, 4, 4, 4, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 4, 4, 37, 37, 40, 40, 40, 40, 40] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 613) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/613 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/613' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1)Cc1ccccc1) `ZINC001444928851.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001444928851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001444928851 none CN(CCNC(=O)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 9, 9, 4, 9, 4, 4, 4, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 5, 5, 5, 2, 4, 4, 30, 35, 36, 36, 36, 36, 36, 30, 30, 30, 29, 29, 24, 24, 9, 4, 4, 4, 4, 4, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 4, 4, 4, 4, 35, 35, 36, 36, 36, 36, 36] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 614) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/614 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/614' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1)Cc1ccccc1) `ZINC001444928851.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001444928851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001444928851 none CN(CCNC(=O)C1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 31, 25, 5, 5, 4, 5, 4, 4, 4, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 2, 4, 4, 32, 37, 40, 40, 40, 40, 40, 32, 32, 32, 31, 31, 25, 25, 5, 4, 4, 4, 4, 4, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 4, 4, 37, 37, 40, 40, 40, 40, 40] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 615) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/615 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/615' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1)Cc1ccccc1) `ZINC001444928851.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001444928851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001444928851 none CN(CCNC(=O)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 9, 9, 4, 9, 4, 4, 4, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 5, 5, 5, 2, 4, 4, 30, 35, 36, 36, 36, 36, 36, 30, 30, 30, 29, 29, 24, 24, 9, 4, 4, 4, 4, 4, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 4, 4, 4, 4, 35, 35, 36, 36, 36, 36, 36] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001444928851 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851 Building ZINC001444928851 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001444928851 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 612) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CN(CCNC(=O)C1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1)Cc1ccccc1) `ZINC001444928851.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001444928851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001444928851 none CN(CCNC(=O)C1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 31, 25, 5, 5, 4, 5, 4, 4, 4, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 2, 4, 4, 32, 37, 40, 40, 40, 40, 40, 32, 32, 32, 31, 31, 25, 25, 5, 4, 4, 4, 4, 4, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 4, 4, 37, 37, 40, 40, 40, 40, 40] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 613) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CN(CCNC(=O)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1)Cc1ccccc1) `ZINC001444928851.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001444928851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001444928851 none CN(CCNC(=O)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 9, 9, 4, 9, 4, 4, 4, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 5, 5, 5, 2, 4, 4, 30, 35, 36, 36, 36, 36, 36, 30, 30, 30, 29, 29, 24, 24, 9, 4, 4, 4, 4, 4, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 4, 4, 4, 4, 35, 35, 36, 36, 36, 36, 36] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 614) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/614: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1)Cc1ccccc1) `ZINC001444928851.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001444928851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001444928851 none CN(CCNC(=O)C1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 31, 25, 5, 5, 4, 5, 4, 4, 4, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 2, 4, 4, 32, 37, 40, 40, 40, 40, 40, 32, 32, 32, 31, 31, 25, 25, 5, 4, 4, 4, 4, 4, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 4, 4, 37, 37, 40, 40, 40, 40, 40] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 615) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/615: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1)Cc1ccccc1) `ZINC001444928851.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001444928851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001444928851 none CN(CCNC(=O)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 9, 9, 4, 9, 4, 4, 4, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 5, 5, 5, 2, 4, 4, 30, 35, 36, 36, 36, 36, 36, 30, 30, 30, 29, 29, 24, 24, 9, 4, 4, 4, 4, 4, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 4, 4, 4, 4, 35, 35, 36, 36, 36, 36, 36] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001444928851 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851 Building ZINC001444928851 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001444928851 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 612) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CN(CCNC(=O)C1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1)Cc1ccccc1) `ZINC001444928851.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001444928851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001444928851 none CN(CCNC(=O)C1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 31, 25, 5, 5, 4, 5, 4, 4, 4, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 2, 4, 4, 32, 37, 40, 40, 40, 40, 40, 32, 32, 32, 31, 31, 25, 25, 5, 4, 4, 4, 4, 4, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 4, 4, 37, 37, 40, 40, 40, 40, 40] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 613) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CN(CCNC(=O)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1)Cc1ccccc1) `ZINC001444928851.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001444928851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001444928851 none CN(CCNC(=O)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 9, 9, 4, 9, 4, 4, 4, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 5, 5, 5, 2, 4, 4, 30, 35, 36, 36, 36, 36, 36, 30, 30, 30, 29, 29, 24, 24, 9, 4, 4, 4, 4, 4, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 4, 4, 4, 4, 35, 35, 36, 36, 36, 36, 36] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 614) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/614: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1)Cc1ccccc1) `ZINC001444928851.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001444928851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001444928851 none CN(CCNC(=O)C1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 31, 25, 5, 5, 4, 5, 4, 4, 4, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 2, 4, 4, 32, 37, 40, 40, 40, 40, 40, 32, 32, 32, 31, 31, 25, 25, 5, 4, 4, 4, 4, 4, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 4, 4, 37, 37, 40, 40, 40, 40, 40] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 615) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/615: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1)Cc1ccccc1) `ZINC001444928851.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001444928851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001444928851 none CN(CCNC(=O)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 9, 9, 4, 9, 4, 4, 4, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 5, 5, 5, 2, 4, 4, 30, 35, 36, 36, 36, 36, 36, 30, 30, 30, 29, 29, 24, 24, 9, 4, 4, 4, 4, 4, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 4, 4, 4, 4, 35, 35, 36, 36, 36, 36, 36] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001444928851 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851 Building ZINC001444928851 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001444928851 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 612) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CN(CCNC(=O)C1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1)Cc1ccccc1) `ZINC001444928851.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001444928851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001444928851 none CN(CCNC(=O)C1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 31, 25, 5, 5, 4, 5, 4, 4, 4, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 2, 4, 4, 32, 37, 40, 40, 40, 40, 40, 32, 32, 32, 31, 31, 25, 25, 5, 4, 4, 4, 4, 4, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 4, 4, 37, 37, 40, 40, 40, 40, 40] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 613) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CN(CCNC(=O)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1)Cc1ccccc1) `ZINC001444928851.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001444928851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001444928851 none CN(CCNC(=O)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 9, 9, 4, 9, 4, 4, 4, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 5, 5, 5, 2, 4, 4, 30, 35, 36, 36, 36, 36, 36, 30, 30, 30, 29, 29, 24, 24, 9, 4, 4, 4, 4, 4, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 4, 4, 4, 4, 35, 35, 36, 36, 36, 36, 36] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 614) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/614: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1)Cc1ccccc1) `ZINC001444928851.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001444928851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001444928851 none CN(CCNC(=O)C1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 31, 25, 5, 5, 4, 5, 4, 4, 4, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 2, 4, 4, 32, 37, 40, 40, 40, 40, 40, 32, 32, 32, 31, 31, 25, 25, 5, 4, 4, 4, 4, 4, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 4, 4, 37, 37, 40, 40, 40, 40, 40] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 615) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/615: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1)Cc1ccccc1) `ZINC001444928851.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001444928851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001444928851 none CN(CCNC(=O)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 9, 9, 4, 9, 4, 4, 4, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 5, 5, 5, 2, 4, 4, 30, 35, 36, 36, 36, 36, 36, 30, 30, 30, 29, 29, 24, 24, 9, 4, 4, 4, 4, 4, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 4, 4, 4, 4, 35, 35, 36, 36, 36, 36, 36] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001444928851 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001444928851 Building ZINC001446387113 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387113' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387113 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001446387113 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387113/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387113 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 616) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/616 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/616' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@@H](c2ccccc2)c2ccccc2CCN1C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001446387113.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001446387113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001446387113 none C[C@H]1[C@@H](c2ccccc2)c2ccccc2CCN1C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 2, 8, 1, 1, 1, 2, 2, 2, 8, 8, 8, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 8, 8, 2, 2, 2, 2] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387113 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387113/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387113 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 617) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/617 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/617' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@@H](c2ccccc2)c2ccccc2CCN1C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001446387113.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001446387113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001446387113 none C[C@H]1[C@@H](c2ccccc2)c2ccccc2CCN1C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 9, 2, 8, 1, 1, 1, 4, 4, 4, 13, 13, 13, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 13, 13, 4, 4, 4, 4] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387113 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001446387113 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387113/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387113/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387113 Building ZINC001446387113 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387113' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387113 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001446387113 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387113/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387113 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 616) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: C[C@H]1[C@@H](c2ccccc2)c2ccccc2CCN1C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001446387113.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001446387113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001446387113 none C[C@H]1[C@@H](c2ccccc2)c2ccccc2CCN1C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 2, 8, 1, 1, 1, 2, 2, 2, 8, 8, 8, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 8, 8, 2, 2, 2, 2] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387113 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387113/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387113 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 617) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: C[C@H]1[C@@H](c2ccccc2)c2ccccc2CCN1C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001446387113.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001446387113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001446387113 none C[C@H]1[C@@H](c2ccccc2)c2ccccc2CCN1C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 9, 2, 8, 1, 1, 1, 4, 4, 4, 13, 13, 13, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 13, 13, 4, 4, 4, 4] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387113 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001446387113 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387113/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387113/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387113 Building ZINC001446387120 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387120' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387120 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001446387120 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387120/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387120 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 618) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/618 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/618' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@H](c2ccccc2)c2ccccc2CCN1C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001446387120.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001446387120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387120/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001446387120 none C[C@H]1[C@H](c2ccccc2)c2ccccc2CCN1C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 12, 12, 11, 12, 12, 11, 11, 11, 11, 11, 11, 11, 11, 9, 1, 9, 1, 1, 1, 4, 4, 4, 15, 15, 15, 4, 4, 4, 11, 11, 11, 12, 12, 11, 12, 12, 11, 11, 11, 11, 11, 11, 11, 11, 4, 15, 15, 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, 52, 53, 54, 55, 56]) total number of confs: 77 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387120 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387120/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387120 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 619) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/619 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/619' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@H](c2ccccc2)c2ccccc2CCN1C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001446387120.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001446387120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387120/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001446387120 none C[C@H]1[C@H](c2ccccc2)c2ccccc2CCN1C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 10, 11, 11, 10, 10, 10, 10, 10, 10, 10, 10, 7, 1, 7, 1, 1, 1, 3, 3, 3, 11, 11, 11, 3, 3, 3, 10, 10, 10, 11, 11, 10, 11, 11, 10, 10, 10, 10, 10, 10, 10, 10, 3, 11, 11, 3, 3, 3, 3] 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]) total number of confs: 62 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387120 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001446387120 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387120/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387120/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387120 Building ZINC001446387120 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387120' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387120 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001446387120 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387120/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387120 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 618) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: C[C@H]1[C@H](c2ccccc2)c2ccccc2CCN1C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001446387120.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001446387120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387120/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001446387120 none C[C@H]1[C@H](c2ccccc2)c2ccccc2CCN1C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 12, 12, 11, 12, 12, 11, 11, 11, 11, 11, 11, 11, 11, 9, 1, 9, 1, 1, 1, 4, 4, 4, 15, 15, 15, 4, 4, 4, 11, 11, 11, 12, 12, 11, 12, 12, 11, 11, 11, 11, 11, 11, 11, 11, 4, 15, 15, 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, 52, 53, 54, 55, 56]) total number of confs: 77 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387120 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387120/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387120 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 619) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: C[C@H]1[C@H](c2ccccc2)c2ccccc2CCN1C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001446387120.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001446387120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387120/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001446387120 none C[C@H]1[C@H](c2ccccc2)c2ccccc2CCN1C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 10, 11, 11, 10, 10, 10, 10, 10, 10, 10, 10, 7, 1, 7, 1, 1, 1, 3, 3, 3, 11, 11, 11, 3, 3, 3, 10, 10, 10, 11, 11, 10, 11, 11, 10, 10, 10, 10, 10, 10, 10, 10, 3, 11, 11, 3, 3, 3, 3] 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]) total number of confs: 62 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387120 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001446387120 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387120/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387120/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387120 Building ZINC001446387129 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387129' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387129 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001446387129 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387129/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387129 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 620) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/620 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/620' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](c2ccccc2)c2ccccc2CCN1C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001446387129.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001446387129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001446387129 none C[C@@H]1[C@H](c2ccccc2)c2ccccc2CCN1C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 2, 9, 1, 1, 1, 2, 2, 2, 8, 8, 8, 2, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 8, 8, 2, 2, 2, 2] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387129 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387129/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387129 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 621) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/621 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/621' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](c2ccccc2)c2ccccc2CCN1C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001446387129.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001446387129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387129/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001446387129 none C[C@@H]1[C@H](c2ccccc2)c2ccccc2CCN1C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 2, 7, 1, 1, 1, 2, 2, 2, 8, 8, 8, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 8, 8, 2, 2, 2, 2] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387129 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001446387129 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387129/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387129/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387129 Building ZINC001446387129 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387129' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387129 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001446387129 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387129/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387129 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 620) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: C[C@@H]1[C@H](c2ccccc2)c2ccccc2CCN1C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001446387129.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001446387129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001446387129 none C[C@@H]1[C@H](c2ccccc2)c2ccccc2CCN1C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 2, 9, 1, 1, 1, 2, 2, 2, 8, 8, 8, 2, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 8, 8, 2, 2, 2, 2] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387129 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387129/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387129 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 621) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: C[C@@H]1[C@H](c2ccccc2)c2ccccc2CCN1C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001446387129.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001446387129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387129/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001446387129 none C[C@@H]1[C@H](c2ccccc2)c2ccccc2CCN1C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 2, 7, 1, 1, 1, 2, 2, 2, 8, 8, 8, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 8, 8, 2, 2, 2, 2] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387129 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001446387129 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387129/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387129/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387129 Building ZINC001446387134 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387134' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387134 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001446387134 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387134/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387134 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 622) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/622 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/622' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](c2ccccc2)c2ccccc2CCN1C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001446387134.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001446387134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387134/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001446387134 none C[C@@H]1[C@@H](c2ccccc2)c2ccccc2CCN1C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 10, 12, 12, 10, 10, 10, 10, 10, 10, 10, 10, 8, 1, 8, 1, 1, 1, 3, 3, 3, 12, 12, 12, 3, 3, 3, 10, 10, 10, 12, 12, 10, 12, 12, 10, 10, 10, 10, 10, 10, 10, 10, 3, 12, 12, 3, 3, 3, 3] 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]) total number of confs: 70 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387134 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387134/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387134 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 623) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/623 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/623' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](c2ccccc2)c2ccccc2CCN1C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001446387134.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001446387134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387134/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001446387134 none C[C@@H]1[C@@H](c2ccccc2)c2ccccc2CCN1C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 12, 13, 13, 12, 13, 13, 12, 12, 12, 12, 12, 12, 12, 12, 10, 1, 10, 1, 1, 1, 5, 5, 5, 14, 14, 14, 5, 5, 5, 12, 12, 12, 13, 13, 12, 13, 13, 12, 12, 12, 12, 12, 12, 12, 12, 5, 14, 14, 5, 5, 5, 5] 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]) total number of confs: 71 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387134 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001446387134 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387134/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387134/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387134 Building ZINC001446387134 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387134' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387134 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001446387134 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387134/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387134 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 622) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: C[C@@H]1[C@@H](c2ccccc2)c2ccccc2CCN1C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001446387134.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001446387134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387134/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001446387134 none C[C@@H]1[C@@H](c2ccccc2)c2ccccc2CCN1C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 10, 12, 12, 10, 10, 10, 10, 10, 10, 10, 10, 8, 1, 8, 1, 1, 1, 3, 3, 3, 12, 12, 12, 3, 3, 3, 10, 10, 10, 12, 12, 10, 12, 12, 10, 10, 10, 10, 10, 10, 10, 10, 3, 12, 12, 3, 3, 3, 3] 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]) total number of confs: 70 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387134 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387134/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387134 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 623) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: C[C@@H]1[C@@H](c2ccccc2)c2ccccc2CCN1C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001446387134.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001446387134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387134/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001446387134 none C[C@@H]1[C@@H](c2ccccc2)c2ccccc2CCN1C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 12, 13, 13, 12, 13, 13, 12, 12, 12, 12, 12, 12, 12, 12, 10, 1, 10, 1, 1, 1, 5, 5, 5, 14, 14, 14, 5, 5, 5, 12, 12, 12, 13, 13, 12, 13, 13, 12, 12, 12, 12, 12, 12, 12, 12, 5, 14, 14, 5, 5, 5, 5] 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]) total number of confs: 71 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387134 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001446387134 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387134/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387134/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446387134 Building ZINC001446598544 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446598544' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446598544 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001446598544 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446598544/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446598544 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 624) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/624 `/scratch/xiaobo/418326/xbt-8058088.46/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)N2CCN(S(=O)(=O)c3ccc(F)c(Cl)c3)CC2)cn1) `ZINC001446598544.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001446598544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446598544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001446598544 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3ccc(F)c(Cl)c3)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 16, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 2, 2, 1, 1, 1, 1, 4, 6, 12, 12, 12, 12, 20, 20, 20, 33, 33, 33, 33, 33, 33, 33, 12, 12, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 12, 12, 12, 12, 33, 33, 33, 12, 12, 12, 12, 2] 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]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446598544 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446598544/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446598544 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 625) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/625 `/scratch/xiaobo/418326/xbt-8058088.46/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)N2CCN(S(=O)(=O)c3ccc(F)c(Cl)c3)CC2)cn1) `ZINC001446598544.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001446598544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446598544/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001446598544 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3ccc(F)c(Cl)c3)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 16, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 7, 7, 5, 5, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 14, 14, 14, 32, 32, 27, 27, 32, 32, 32, 7, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 7, 7, 7, 7, 32, 32, 32, 7, 7, 7, 7, 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, 50, 51]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446598544 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001446598544 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446598544/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446598544/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446598544 Building ZINC001446598544 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446598544' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446598544 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001446598544 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446598544/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446598544 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 624) grep: /scratch/xiaobo/418326/xbt-8058088.46/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)N2CCN(S(=O)(=O)c3ccc(F)c(Cl)c3)CC2)cn1) `ZINC001446598544.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001446598544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446598544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001446598544 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3ccc(F)c(Cl)c3)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 16, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 2, 2, 1, 1, 1, 1, 4, 6, 12, 12, 12, 12, 20, 20, 20, 33, 33, 33, 33, 33, 33, 33, 12, 12, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 12, 12, 12, 12, 33, 33, 33, 12, 12, 12, 12, 2] 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]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446598544 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446598544/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446598544 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 625) grep: /scratch/xiaobo/418326/xbt-8058088.46/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)N2CCN(S(=O)(=O)c3ccc(F)c(Cl)c3)CC2)cn1) `ZINC001446598544.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001446598544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446598544/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001446598544 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3ccc(F)c(Cl)c3)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 16, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 7, 7, 5, 5, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 14, 14, 14, 32, 32, 27, 27, 32, 32, 32, 7, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 7, 7, 7, 7, 32, 32, 32, 7, 7, 7, 7, 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, 50, 51]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446598544 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001446598544 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446598544/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446598544/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446598544 Building ZINC001446719329 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446719329' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446719329 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001446719329 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446719329/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446719329 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 626) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/626 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/626' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1NS(=O)(=O)c1ccc(O)c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c1) `ZINC001446719329.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001446719329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446719329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001446719329 none COc1ccccc1NS(=O)(=O)c1ccc(O)c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 33, 31, 33, 33, 22, 8, 5, 8, 8, 5, 4, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 5, 33, 33, 33, 33, 33, 33, 33, 22, 5, 5, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5] 100 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446719329 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446719329/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446719329 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 627) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/627 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/627' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1NS(=O)(=O)c1ccc(O)c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c1) `ZINC001446719329.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001446719329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446719329/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001446719329 none COc1ccccc1NS(=O)(=O)c1ccc(O)c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 34, 32, 34, 34, 22, 8, 5, 8, 8, 5, 4, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 5, 34, 34, 34, 34, 34, 34, 34, 22, 5, 5, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5] 100 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446719329 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001446719329 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446719329/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446719329/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446719329 Building ZINC001446719329 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446719329' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446719329 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001446719329 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446719329/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446719329 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 626) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccccc1NS(=O)(=O)c1ccc(O)c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c1) `ZINC001446719329.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001446719329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446719329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001446719329 none COc1ccccc1NS(=O)(=O)c1ccc(O)c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 33, 31, 33, 33, 22, 8, 5, 8, 8, 5, 4, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 5, 33, 33, 33, 33, 33, 33, 33, 22, 5, 5, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5] 100 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446719329 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446719329/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446719329 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 627) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccccc1NS(=O)(=O)c1ccc(O)c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c1) `ZINC001446719329.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001446719329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446719329/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001446719329 none COc1ccccc1NS(=O)(=O)c1ccc(O)c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 34, 32, 34, 34, 22, 8, 5, 8, 8, 5, 4, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 5, 34, 34, 34, 34, 34, 34, 34, 22, 5, 5, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5] 100 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446719329 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001446719329 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446719329/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446719329/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001446719329 Building ZINC001448095235 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448095235' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448095235 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001448095235 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448095235/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448095235 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 628) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/628 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/628' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1OC[C@H]1CCCCO1) `ZINC001448095235.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001448095235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448095235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001448095235 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1OC[C@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 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, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 4, 5, 5, 5, 16, 31, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 4, 4, 1, 2, 5, 5, 5, 27, 27, 33, 33, 33, 33, 33, 33, 33, 33] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 8, 9, 10, 11, 12, 34, 37, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448095235 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448095235/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448095235 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 629) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/629 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/629' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1OC[C@H]1CCCCO1) `ZINC001448095235.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001448095235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448095235/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001448095235 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1OC[C@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 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, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 15, 26, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 4, 4, 1, 2, 4, 4, 4, 22, 22, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 8, 9, 10, 11, 12, 34, 37, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 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/418326/xbt-8058088.46/working/building/ZINC001448095235 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001448095235 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448095235/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448095235/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448095235 Building ZINC001448095235 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448095235' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448095235 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001448095235 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448095235/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448095235 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 628) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1OC[C@H]1CCCCO1) `ZINC001448095235.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001448095235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448095235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001448095235 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1OC[C@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 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, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 4, 5, 5, 5, 16, 31, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 4, 4, 1, 2, 5, 5, 5, 27, 27, 33, 33, 33, 33, 33, 33, 33, 33] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 8, 9, 10, 11, 12, 34, 37, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448095235 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448095235/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448095235 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 629) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1OC[C@H]1CCCCO1) `ZINC001448095235.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001448095235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448095235/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001448095235 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1OC[C@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 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, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 15, 26, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 4, 4, 1, 2, 4, 4, 4, 22, 22, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 8, 9, 10, 11, 12, 34, 37, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 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/418326/xbt-8058088.46/working/building/ZINC001448095235 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001448095235 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448095235/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448095235/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448095235 Building ZINC001448095237 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448095237' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448095237 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001448095237 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448095237/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448095237 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 630) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/630 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/630' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1OC[C@@H]1CCCCO1) `ZINC001448095237.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001448095237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448095237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001448095237 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1OC[C@@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 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, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 16, 27, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 4, 4, 1, 2, 4, 4, 4, 23, 23, 29, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 8, 9, 10, 11, 12, 34, 37, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 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/418326/xbt-8058088.46/working/building/ZINC001448095237 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448095237/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448095237 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 631) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/631 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/631' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1OC[C@@H]1CCCCO1) `ZINC001448095237.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001448095237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448095237/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001448095237 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1OC[C@@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 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, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 5, 5, 5, 16, 30, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 4, 4, 1, 2, 5, 5, 5, 27, 27, 32, 32, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 8, 9, 10, 11, 12, 34, 37, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448095237 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001448095237 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448095237/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448095237/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448095237 Building ZINC001448095237 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448095237' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448095237 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001448095237 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448095237/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448095237 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 630) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1OC[C@@H]1CCCCO1) `ZINC001448095237.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001448095237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448095237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001448095237 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1OC[C@@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 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, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 16, 27, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 4, 4, 1, 2, 4, 4, 4, 23, 23, 29, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 8, 9, 10, 11, 12, 34, 37, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 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/418326/xbt-8058088.46/working/building/ZINC001448095237 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448095237/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448095237 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 631) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1OC[C@@H]1CCCCO1) `ZINC001448095237.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001448095237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448095237/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001448095237 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1OC[C@@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 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, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 5, 5, 5, 16, 30, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 4, 4, 1, 2, 5, 5, 5, 27, 27, 32, 32, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 8, 9, 10, 11, 12, 34, 37, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448095237 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001448095237 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448095237/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448095237/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448095237 Building ZINC001448632684 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448632684' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448632684 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001448632684 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448632684/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448632684 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 632) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/632 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/632' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCn3c(nnc3c3cncc(Br)c3)C2)cn1) `ZINC001448632684.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001448632684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448632684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001448632684 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCn3c(nnc3c3cncc(Br)c3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 8, 8, 1, 1, 1, 8, 1, 1, 17, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 2, 2, 1, 1, 1, 2, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 31, 31, 31, 31, 31, 31, 6, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 6, 6, 6, 6, 31, 31, 31, 6, 6, 2] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448632684 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448632684/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448632684 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 633) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/633 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/633' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCn3c(nnc3c3cncc(Br)c3)C2)cn1) `ZINC001448632684.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001448632684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448632684/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001448632684 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCn3c(nnc3c3cncc(Br)c3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 8, 8, 1, 1, 1, 8, 1, 1, 17, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 4, 2, 2, 1, 1, 1, 2, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 29, 29, 5, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 5, 5, 5, 5, 29, 29, 29, 5, 5, 2] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448632684 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001448632684 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448632684/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448632684/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448632684 Building ZINC001448632684 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448632684' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448632684 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001448632684 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448632684/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448632684 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 632) grep: /scratch/xiaobo/418326/xbt-8058088.46/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(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCn3c(nnc3c3cncc(Br)c3)C2)cn1) `ZINC001448632684.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001448632684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448632684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001448632684 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCn3c(nnc3c3cncc(Br)c3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 8, 8, 1, 1, 1, 8, 1, 1, 17, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 2, 2, 1, 1, 1, 2, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 31, 31, 31, 31, 31, 31, 6, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 6, 6, 6, 6, 31, 31, 31, 6, 6, 2] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448632684 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448632684/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448632684 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 633) grep: /scratch/xiaobo/418326/xbt-8058088.46/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(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCn3c(nnc3c3cncc(Br)c3)C2)cn1) `ZINC001448632684.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001448632684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448632684/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001448632684 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCn3c(nnc3c3cncc(Br)c3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 8, 8, 1, 1, 1, 8, 1, 1, 17, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 4, 2, 2, 1, 1, 1, 2, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 29, 29, 5, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 5, 5, 5, 5, 29, 29, 29, 5, 5, 2] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448632684 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001448632684 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448632684/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448632684/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448632684 Building ZINC001448775053 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448775053' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448775053 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001448775053 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448775053/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448775053 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 634) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/634 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/634' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1c1ncc(c2cccc(F)c2)[nH]1) `ZINC001448775053.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001448775053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448775053/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001448775053 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1c1ncc(c2cccc(F)c2)[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 8, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 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, 7, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16, 16, 16, 3, 3, 2, 2, 2, 2, 7, 7, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16] 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]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448775053 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448775053/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448775053 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 635) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/635 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/635' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1c1ncc(c2cccc(F)c2)[nH]1) `ZINC001448775053.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001448775053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448775053/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001448775053 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1c1ncc(c2cccc(F)c2)[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 8, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 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, 6, 2, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 20, 20, 20, 20, 20, 20, 7, 7, 2, 2, 2, 2, 6, 6, 2, 5, 5, 5, 5, 5, 5, 5, 5, 7, 20, 20, 20, 20] 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]) total number of confs: 54 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448775053 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001448775053 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448775053/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448775053/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448775053 Building ZINC001448775053 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448775053' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448775053 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001448775053 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448775053/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448775053 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 634) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1c1ncc(c2cccc(F)c2)[nH]1) `ZINC001448775053.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001448775053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448775053/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001448775053 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1c1ncc(c2cccc(F)c2)[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 8, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 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, 7, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16, 16, 16, 3, 3, 2, 2, 2, 2, 7, 7, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16] 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]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448775053 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448775053/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448775053 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 635) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1c1ncc(c2cccc(F)c2)[nH]1) `ZINC001448775053.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001448775053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448775053/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001448775053 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1c1ncc(c2cccc(F)c2)[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 8, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 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, 6, 2, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 20, 20, 20, 20, 20, 20, 7, 7, 2, 2, 2, 2, 6, 6, 2, 5, 5, 5, 5, 5, 5, 5, 5, 7, 20, 20, 20, 20] 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]) total number of confs: 54 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448775053 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001448775053 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448775053/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448775053/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448775053 Building ZINC001448775059 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448775059' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448775059 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001448775059 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448775059/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448775059 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 636) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/636 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/636' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1c1ncc(c2cccc(F)c2)[nH]1) `ZINC001448775059.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001448775059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448775059/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001448775059 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1c1ncc(c2cccc(F)c2)[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 8, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25, 8, 8, 1, 1, 1, 1, 4, 4, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 25, 25, 25, 25] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 8, 9, 10, 11, 12, 2, 40, 3, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448775059 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448775059/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448775059 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 637) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/637 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/637' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1c1ncc(c2cccc(F)c2)[nH]1) `ZINC001448775059.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001448775059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448775059/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001448775059 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1c1ncc(c2cccc(F)c2)[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 8, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 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, 7, 2, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 13, 13, 13, 4, 4, 2, 2, 2, 2, 7, 7, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 13] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448775059 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001448775059 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448775059/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448775059/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448775059 Building ZINC001448775059 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448775059' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448775059 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001448775059 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448775059/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448775059 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 636) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/636: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1c1ncc(c2cccc(F)c2)[nH]1) `ZINC001448775059.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001448775059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448775059/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001448775059 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1c1ncc(c2cccc(F)c2)[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 8, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25, 8, 8, 1, 1, 1, 1, 4, 4, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 25, 25, 25, 25] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 8, 9, 10, 11, 12, 2, 40, 3, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448775059 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448775059/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448775059 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 637) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/637: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1c1ncc(c2cccc(F)c2)[nH]1) `ZINC001448775059.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001448775059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448775059/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001448775059 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1c1ncc(c2cccc(F)c2)[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 8, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 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, 7, 2, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 13, 13, 13, 4, 4, 2, 2, 2, 2, 7, 7, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 13] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448775059 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001448775059 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448775059/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448775059/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001448775059 Building ZINC001449056992 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449056992' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449056992 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001449056992 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449056992/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449056992 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 638) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/638 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/638' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N(Cc1cccc(Br)c1)CC1CC1) `ZINC001449056992.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001449056992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449056992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001449056992 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N(Cc1cccc(Br)c1)CC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 1, 1, 1, 1, 2, 5, 12, 12, 10, 12, 12, 12, 2, 4, 7, 7, 1, 1, 1, 1, 4, 4, 1, 5, 5, 12, 12, 12, 12, 4, 4, 7, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30] set([5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 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/418326/xbt-8058088.46/working/building/ZINC001449056992 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449056992/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449056992 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 639) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/639 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/639' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N(Cc1cccc(Br)c1)CC1CC1) `ZINC001449056992.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001449056992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449056992/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001449056992 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N(Cc1cccc(Br)c1)CC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 1, 1, 2, 2, 3, 8, 19, 19, 19, 19, 19, 19, 3, 7, 9, 9, 1, 1, 1, 1, 4, 4, 1, 8, 8, 19, 19, 19, 19, 7, 7, 9, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 8, 9, 10, 11, 12, 27, 28, 29, 30] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449056992 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001449056992 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449056992/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449056992/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449056992 Building ZINC001449056992 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449056992' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449056992 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001449056992 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449056992/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449056992 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 638) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N(Cc1cccc(Br)c1)CC1CC1) `ZINC001449056992.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001449056992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449056992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001449056992 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N(Cc1cccc(Br)c1)CC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 1, 1, 1, 1, 2, 5, 12, 12, 10, 12, 12, 12, 2, 4, 7, 7, 1, 1, 1, 1, 4, 4, 1, 5, 5, 12, 12, 12, 12, 4, 4, 7, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30] set([5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 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/418326/xbt-8058088.46/working/building/ZINC001449056992 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449056992/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449056992 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 639) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N(Cc1cccc(Br)c1)CC1CC1) `ZINC001449056992.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001449056992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449056992/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001449056992 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N(Cc1cccc(Br)c1)CC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 1, 1, 2, 2, 3, 8, 19, 19, 19, 19, 19, 19, 3, 7, 9, 9, 1, 1, 1, 1, 4, 4, 1, 8, 8, 19, 19, 19, 19, 7, 7, 9, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 8, 9, 10, 11, 12, 27, 28, 29, 30] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449056992 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001449056992 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449056992/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449056992/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449056992 Building ZINC001449293244 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449293244' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449293244 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001449293244 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449293244/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449293244 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 640) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/640 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/640' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)Oc1ccc(Br)cc1) `ZINC001449293244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001449293244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449293244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001449293244 none COC(=O)[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)Oc1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.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', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 18, 8, 10, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 10, 18, 21, 21, 21, 21, 21, 21, 18, 18, 18, 8, 8, 2, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 21, 21, 21, 21] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449293244 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449293244/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449293244 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 641) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/641 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/641' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)Oc1ccc(Br)cc1) `ZINC001449293244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001449293244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449293244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001449293244 none COC(=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)Oc1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.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', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 7, 15, 5, 7, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 7, 12, 18, 18, 18, 18, 18, 18, 15, 15, 15, 5, 5, 2, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 18, 18, 18, 18] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449293244 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001449293244 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449293244/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449293244/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449293244 Building ZINC001449293244 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449293244' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449293244 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001449293244 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449293244/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449293244 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 640) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/640: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)Oc1ccc(Br)cc1) `ZINC001449293244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001449293244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449293244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001449293244 none COC(=O)[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)Oc1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.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', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 18, 8, 10, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 10, 18, 21, 21, 21, 21, 21, 21, 18, 18, 18, 8, 8, 2, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 21, 21, 21, 21] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449293244 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449293244/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449293244 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 641) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/641: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)Oc1ccc(Br)cc1) `ZINC001449293244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001449293244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449293244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001449293244 none COC(=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)Oc1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.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', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 7, 15, 5, 7, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 7, 12, 18, 18, 18, 18, 18, 18, 15, 15, 15, 5, 5, 2, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 18, 18, 18, 18] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449293244 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001449293244 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449293244/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449293244/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449293244 Building ZINC001449293248 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449293248' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449293248 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001449293248 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449293248/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449293248 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 642) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/642 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/642' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)Oc1ccc(Br)cc1) `ZINC001449293248.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001449293248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449293248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001449293248 none COC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)Oc1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.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', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 8, 16, 5, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 8, 13, 19, 19, 14, 15, 19, 19, 16, 16, 16, 5, 5, 2, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 19, 19, 19, 19] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449293248 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449293248/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449293248 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 643) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/643 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/643' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)Oc1ccc(Br)cc1) `ZINC001449293248.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001449293248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449293248/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001449293248 none COC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)Oc1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.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', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 18, 8, 10, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 10, 18, 21, 21, 18, 18, 21, 21, 18, 18, 18, 8, 8, 2, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 21, 21, 21, 21] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449293248 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001449293248 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449293248/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449293248/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449293248 Building ZINC001449293248 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449293248' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449293248 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001449293248 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449293248/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449293248 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 642) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)Oc1ccc(Br)cc1) `ZINC001449293248.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001449293248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449293248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001449293248 none COC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)Oc1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.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', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 8, 16, 5, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 8, 13, 19, 19, 14, 15, 19, 19, 16, 16, 16, 5, 5, 2, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 19, 19, 19, 19] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449293248 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449293248/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449293248 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 643) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)Oc1ccc(Br)cc1) `ZINC001449293248.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001449293248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449293248/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001449293248 none COC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)Oc1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.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', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 18, 8, 10, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 10, 18, 21, 21, 18, 18, 21, 21, 18, 18, 18, 8, 8, 2, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 21, 21, 21, 21] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449293248 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001449293248 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449293248/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449293248/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001449293248 Building ZINC001450608819 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001450608819 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 644) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/644 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/644' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)CCN1C(=O)c2ccccc2C1=O) `ZINC001450608819.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001450608819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001450608819 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)CCN1C(=O)c2ccccc2C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 2, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 24, 31, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 15, 15, 15, 11, 11, 11, 11, 4, 4, 4, 4, 4, 4, 4, 24, 24, 31, 31, 33, 33, 33, 33] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 645) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/645 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/645' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)CCN1C(=O)c2ccccc2C1=O) `ZINC001450608819.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001450608819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001450608819 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)CCN1C(=O)c2ccccc2C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 2, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 24, 31, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 15, 15, 15, 11, 11, 11, 11, 4, 4, 4, 4, 4, 4, 4, 24, 24, 31, 31, 33, 33, 33, 33] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 646) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/646 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/646' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)CCN1C(=O)c2ccccc2C1=O) `ZINC001450608819.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001450608819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001450608819 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)CCN1C(=O)c2ccccc2C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 2, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 24, 31, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 15, 11, 11, 11, 11, 4, 4, 4, 4, 4, 4, 4, 24, 24, 31, 31, 32, 32, 32, 32] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 647) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/647 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/647' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)CCN1C(=O)c2ccccc2C1=O) `ZINC001450608819.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001450608819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001450608819 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)CCN1C(=O)c2ccccc2C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 2, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 24, 31, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 15, 11, 11, 11, 11, 4, 4, 4, 4, 4, 4, 4, 24, 24, 31, 31, 32, 32, 32, 32] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001450608819 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819 Building ZINC001450608819 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001450608819 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 644) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/644: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)CCN1C(=O)c2ccccc2C1=O) `ZINC001450608819.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001450608819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001450608819 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)CCN1C(=O)c2ccccc2C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 2, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 24, 31, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 15, 15, 15, 11, 11, 11, 11, 4, 4, 4, 4, 4, 4, 4, 24, 24, 31, 31, 33, 33, 33, 33] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 645) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/645: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)CCN1C(=O)c2ccccc2C1=O) `ZINC001450608819.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001450608819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001450608819 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)CCN1C(=O)c2ccccc2C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 2, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 24, 31, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 15, 15, 15, 11, 11, 11, 11, 4, 4, 4, 4, 4, 4, 4, 24, 24, 31, 31, 33, 33, 33, 33] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 646) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/646: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)CCN1C(=O)c2ccccc2C1=O) `ZINC001450608819.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001450608819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001450608819 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)CCN1C(=O)c2ccccc2C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 2, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 24, 31, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 15, 11, 11, 11, 11, 4, 4, 4, 4, 4, 4, 4, 24, 24, 31, 31, 32, 32, 32, 32] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 647) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/647: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)CCN1C(=O)c2ccccc2C1=O) `ZINC001450608819.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001450608819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001450608819 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)CCN1C(=O)c2ccccc2C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 2, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 24, 31, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 15, 11, 11, 11, 11, 4, 4, 4, 4, 4, 4, 4, 24, 24, 31, 31, 32, 32, 32, 32] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001450608819 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819 Building ZINC001450608819 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001450608819 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 644) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/644: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)CCN1C(=O)c2ccccc2C1=O) `ZINC001450608819.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001450608819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001450608819 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)CCN1C(=O)c2ccccc2C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 2, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 24, 31, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 15, 15, 15, 11, 11, 11, 11, 4, 4, 4, 4, 4, 4, 4, 24, 24, 31, 31, 33, 33, 33, 33] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 645) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/645: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)CCN1C(=O)c2ccccc2C1=O) `ZINC001450608819.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001450608819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001450608819 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)CCN1C(=O)c2ccccc2C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 2, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 24, 31, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 15, 15, 15, 11, 11, 11, 11, 4, 4, 4, 4, 4, 4, 4, 24, 24, 31, 31, 33, 33, 33, 33] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 646) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/646: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)CCN1C(=O)c2ccccc2C1=O) `ZINC001450608819.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001450608819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001450608819 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)CCN1C(=O)c2ccccc2C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 2, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 24, 31, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 15, 11, 11, 11, 11, 4, 4, 4, 4, 4, 4, 4, 24, 24, 31, 31, 32, 32, 32, 32] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 647) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/647: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)CCN1C(=O)c2ccccc2C1=O) `ZINC001450608819.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001450608819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001450608819 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)CCN1C(=O)c2ccccc2C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 2, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 24, 31, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 15, 11, 11, 11, 11, 4, 4, 4, 4, 4, 4, 4, 24, 24, 31, 31, 32, 32, 32, 32] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001450608819 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819 Building ZINC001450608819 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001450608819 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 644) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/644: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)CCN1C(=O)c2ccccc2C1=O) `ZINC001450608819.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001450608819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001450608819 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)CCN1C(=O)c2ccccc2C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 2, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 24, 31, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 15, 15, 15, 11, 11, 11, 11, 4, 4, 4, 4, 4, 4, 4, 24, 24, 31, 31, 33, 33, 33, 33] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 645) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/645: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)CCN1C(=O)c2ccccc2C1=O) `ZINC001450608819.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001450608819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001450608819 none CN(CCN(C)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)CCN1C(=O)c2ccccc2C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 2, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 24, 31, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 15, 15, 15, 11, 11, 11, 11, 4, 4, 4, 4, 4, 4, 4, 24, 24, 31, 31, 33, 33, 33, 33] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 646) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/646: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)CCN1C(=O)c2ccccc2C1=O) `ZINC001450608819.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001450608819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001450608819 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)CCN1C(=O)c2ccccc2C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 2, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 24, 31, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 15, 11, 11, 11, 11, 4, 4, 4, 4, 4, 4, 4, 24, 24, 31, 31, 32, 32, 32, 32] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 647) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/647: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)CCN1C(=O)c2ccccc2C1=O) `ZINC001450608819.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001450608819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001450608819 none CN(CCN(C)C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)CCN1C(=O)c2ccccc2C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 2, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 24, 31, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 15, 11, 11, 11, 11, 4, 4, 4, 4, 4, 4, 4, 24, 24, 31, 31, 32, 32, 32, 32] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001450608819 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001450608819 Building ZINC001453777531 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453777531' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453777531 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001453777531 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453777531/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453777531 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 648) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/648 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/648' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@]2(C1)c1[nH]cnc1CCN2C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC001453777531.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001453777531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453777531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001453777531 none CC(C)(C)OC(=O)N1CC[C@@]2(C1)c1[nH]cnc1CCN2C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)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', 'C.2', 'N.pl3', 'H', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 6, 1, 8, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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] 0 hydrogens 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, 33, 35, 35, 17, 8, 17, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 8, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 4, 35, 35, 35, 35, 35, 35, 35, 35, 35, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453777531 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453777531/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453777531 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 649) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/649 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/649' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@]2(C1)c1[nH]cnc1CCN2C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC001453777531.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001453777531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453777531/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001453777531 none CC(C)(C)OC(=O)N1CC[C@@]2(C1)c1[nH]cnc1CCN2C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)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', 'C.2', 'N.pl3', 'H', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 6, 1, 8, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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] 0 hydrogens 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, 17, 5, 17, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 4, 30, 30, 30, 30, 30, 30, 30, 30, 30, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453777531 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001453777531 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453777531/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453777531/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453777531 Building ZINC001453777531 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453777531' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453777531 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001453777531 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453777531/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453777531 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 648) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC(C)(C)OC(=O)N1CC[C@@]2(C1)c1[nH]cnc1CCN2C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC001453777531.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001453777531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453777531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001453777531 none CC(C)(C)OC(=O)N1CC[C@@]2(C1)c1[nH]cnc1CCN2C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)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', 'C.2', 'N.pl3', 'H', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 6, 1, 8, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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] 0 hydrogens 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, 33, 35, 35, 17, 8, 17, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 8, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 4, 35, 35, 35, 35, 35, 35, 35, 35, 35, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453777531 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453777531/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453777531 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 649) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC(C)(C)OC(=O)N1CC[C@@]2(C1)c1[nH]cnc1CCN2C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC001453777531.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001453777531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453777531/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001453777531 none CC(C)(C)OC(=O)N1CC[C@@]2(C1)c1[nH]cnc1CCN2C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)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', 'C.2', 'N.pl3', 'H', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 6, 1, 8, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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] 0 hydrogens 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, 17, 5, 17, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 4, 30, 30, 30, 30, 30, 30, 30, 30, 30, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453777531 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001453777531 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453777531/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453777531/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453777531 Building ZINC001453777532 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453777532' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453777532 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001453777532 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453777532/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453777532 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 650) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/650 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/650' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@]2(C1)c1[nH]cnc1CCN2C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC001453777532.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001453777532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453777532/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001453777532 none CC(C)(C)OC(=O)N1CC[C@]2(C1)c1[nH]cnc1CCN2C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)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', 'C.2', 'N.pl3', 'H', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 6, 1, 8, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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] 0 hydrogens 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, 27, 29, 29, 17, 6, 17, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 4, 4, 4, 4, 8, 8, 8, 4, 29, 29, 29, 29, 29, 29, 29, 29, 29, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453777532 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453777532/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453777532 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 651) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/651 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/651' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@]2(C1)c1[nH]cnc1CCN2C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC001453777532.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001453777532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453777532/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001453777532 none CC(C)(C)OC(=O)N1CC[C@]2(C1)c1[nH]cnc1CCN2C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)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', 'C.2', 'N.pl3', 'H', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 6, 1, 8, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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] 0 hydrogens 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, 14, 8, 14, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 8, 1, 1, 1, 6, 6, 6, 6, 8, 8, 8, 6, 30, 30, 30, 30, 30, 30, 30, 30, 30, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453777532 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001453777532 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453777532/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453777532/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453777532 Building ZINC001453777532 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453777532' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453777532 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001453777532 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453777532/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453777532 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 650) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC(C)(C)OC(=O)N1CC[C@]2(C1)c1[nH]cnc1CCN2C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC001453777532.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001453777532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453777532/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001453777532 none CC(C)(C)OC(=O)N1CC[C@]2(C1)c1[nH]cnc1CCN2C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)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', 'C.2', 'N.pl3', 'H', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 6, 1, 8, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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] 0 hydrogens 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, 27, 29, 29, 17, 6, 17, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 4, 4, 4, 4, 8, 8, 8, 4, 29, 29, 29, 29, 29, 29, 29, 29, 29, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453777532 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453777532/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453777532 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 651) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC(C)(C)OC(=O)N1CC[C@]2(C1)c1[nH]cnc1CCN2C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC001453777532.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001453777532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453777532/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001453777532 none CC(C)(C)OC(=O)N1CC[C@]2(C1)c1[nH]cnc1CCN2C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)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', 'C.2', 'N.pl3', 'H', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 6, 1, 8, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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] 0 hydrogens 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, 14, 8, 14, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 8, 1, 1, 1, 6, 6, 6, 6, 8, 8, 8, 6, 30, 30, 30, 30, 30, 30, 30, 30, 30, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453777532 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001453777532 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453777532/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453777532/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453777532 Building ZINC001453815471 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453815471' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453815471 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001453815471 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453815471/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453815471 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 652) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/652 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/652' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@]1(C)Cc1ccccc1C(F)(F)F) `ZINC001453815471.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001453815471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453815471/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001453815471 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@]1(C)Cc1ccccc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 9, 4, 1, 1, 1, 1, 3, 5, 9, 9, 9, 9, 9, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4, 4, 4, 4, 9, 9, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 62 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453815471 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453815471/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453815471 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 653) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/653 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/653' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@]1(C)Cc1ccccc1C(F)(F)F) `ZINC001453815471.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001453815471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453815471/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001453815471 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@]1(C)Cc1ccccc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 12, 4, 1, 1, 1, 1, 3, 4, 6, 6, 6, 6, 6, 6, 15, 16, 16, 16, 16, 16, 16, 16, 16, 16, 4, 4, 4, 4, 12, 12, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 16, 16, 16, 16] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453815471 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001453815471 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453815471/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453815471/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453815471 Building ZINC001453815471 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453815471' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453815471 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001453815471 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453815471/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453815471 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 652) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@]1(C)Cc1ccccc1C(F)(F)F) `ZINC001453815471.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001453815471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453815471/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001453815471 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@]1(C)Cc1ccccc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 9, 4, 1, 1, 1, 1, 3, 5, 9, 9, 9, 9, 9, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4, 4, 4, 4, 9, 9, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 62 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453815471 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453815471/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453815471 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 653) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@]1(C)Cc1ccccc1C(F)(F)F) `ZINC001453815471.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001453815471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453815471/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001453815471 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@]1(C)Cc1ccccc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 12, 4, 1, 1, 1, 1, 3, 4, 6, 6, 6, 6, 6, 6, 15, 16, 16, 16, 16, 16, 16, 16, 16, 16, 4, 4, 4, 4, 12, 12, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 16, 16, 16, 16] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453815471 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001453815471 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453815471/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453815471/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453815471 Building ZINC001453815482 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453815482' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453815482 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001453815482 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453815482/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453815482 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 654) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/654 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/654' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC[C@]1(C)Cc1ccccc1C(F)(F)F) `ZINC001453815482.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001453815482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453815482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001453815482 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC[C@]1(C)Cc1ccccc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 12, 4, 1, 1, 1, 1, 3, 4, 6, 6, 6, 6, 6, 6, 14, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4, 4, 4, 4, 12, 12, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 15, 15, 14, 15] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453815482 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453815482/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453815482 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 655) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/655 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/655' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@]1(C)Cc1ccccc1C(F)(F)F) `ZINC001453815482.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001453815482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453815482/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001453815482 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@]1(C)Cc1ccccc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 10, 10, 10, 4, 1, 1, 1, 1, 3, 5, 9, 9, 9, 9, 9, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4, 4, 4, 4, 10, 10, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 68 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453815482 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001453815482 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453815482/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453815482/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453815482 Building ZINC001453815482 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453815482' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453815482 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001453815482 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453815482/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453815482 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 654) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC[C@]1(C)Cc1ccccc1C(F)(F)F) `ZINC001453815482.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001453815482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453815482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001453815482 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC[C@]1(C)Cc1ccccc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 12, 4, 1, 1, 1, 1, 3, 4, 6, 6, 6, 6, 6, 6, 14, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4, 4, 4, 4, 12, 12, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 15, 15, 14, 15] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453815482 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453815482/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453815482 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 655) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@]1(C)Cc1ccccc1C(F)(F)F) `ZINC001453815482.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001453815482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453815482/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001453815482 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@]1(C)Cc1ccccc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 10, 10, 10, 4, 1, 1, 1, 1, 3, 5, 9, 9, 9, 9, 9, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4, 4, 4, 4, 10, 10, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 68 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453815482 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001453815482 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453815482/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453815482/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001453815482 Building ZINC001455109356 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001455109356' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001455109356 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455109356 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001455109356/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001455109356 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 656) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/656 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/656' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](N2C(=O)O[C@H]3CN(C(=O)OC(C)(C)C)C[C@H]32)C1) `ZINC001455109356.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455109356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001455109356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001455109356 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](N2C(=O)O[C@H]3CN(C(=O)OC(C)(C)C)C[C@H]32)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.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 12, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 7, 7, 7, 7, 11, 23, 23, 23, 23, 23, 23, 23, 23, 35, 35, 50, 50, 50, 50, 23, 23, 23, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 7, 40, 41, 10, 39, 8, 9, 4, 6, 5] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 112 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001455109356 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001455109356/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001455109356 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 657) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/657 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/657' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H](N2C(=O)O[C@H]3CN(C(=O)OC(C)(C)C)C[C@H]32)C1) `ZINC001455109356.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455109356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001455109356/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001455109356 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H](N2C(=O)O[C@H]3CN(C(=O)OC(C)(C)C)C[C@H]32)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.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 12, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 5, 8, 8, 8, 8, 10, 21, 21, 21, 21, 21, 21, 21, 21, 38, 38, 50, 50, 50, 50, 21, 21, 21, 8, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 8, 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, 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: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001455109356 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001455109356 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001455109356/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001455109356/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001455109356 Building ZINC001455109356 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001455109356' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001455109356 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455109356 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001455109356/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001455109356 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 656) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](N2C(=O)O[C@H]3CN(C(=O)OC(C)(C)C)C[C@H]32)C1) `ZINC001455109356.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455109356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001455109356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001455109356 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](N2C(=O)O[C@H]3CN(C(=O)OC(C)(C)C)C[C@H]32)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.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 12, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 7, 7, 7, 7, 11, 23, 23, 23, 23, 23, 23, 23, 23, 35, 35, 50, 50, 50, 50, 23, 23, 23, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 7, 40, 41, 10, 39, 8, 9, 4, 6, 5] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 112 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001455109356 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001455109356/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001455109356 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 657) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H](N2C(=O)O[C@H]3CN(C(=O)OC(C)(C)C)C[C@H]32)C1) `ZINC001455109356.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455109356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001455109356/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001455109356 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H](N2C(=O)O[C@H]3CN(C(=O)OC(C)(C)C)C[C@H]32)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.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 12, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 5, 8, 8, 8, 8, 10, 21, 21, 21, 21, 21, 21, 21, 21, 38, 38, 50, 50, 50, 50, 21, 21, 21, 8, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 8, 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, 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: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001455109356 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001455109356 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001455109356/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001455109356/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001455109356 Building ZINC001455109365 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001455109365' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001455109365 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455109365 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001455109365/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001455109365 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 658) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/658 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/658' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](N2C(=O)O[C@H]3CN(C(=O)OC(C)(C)C)C[C@H]32)C1) `ZINC001455109365.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455109365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001455109365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001455109365 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](N2C(=O)O[C@H]3CN(C(=O)OC(C)(C)C)C[C@H]32)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.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 12, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 4, 8, 8, 8, 8, 10, 22, 22, 22, 22, 22, 22, 22, 22, 36, 36, 50, 50, 50, 50, 22, 22, 22, 8, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 8, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 116 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001455109365 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001455109365/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001455109365 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 659) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/659 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/659' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](N2C(=O)O[C@H]3CN(C(=O)OC(C)(C)C)C[C@H]32)C1) `ZINC001455109365.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455109365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001455109365/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001455109365 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](N2C(=O)O[C@H]3CN(C(=O)OC(C)(C)C)C[C@H]32)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.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 12, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 6, 6, 6, 6, 10, 26, 26, 26, 26, 26, 26, 26, 26, 41, 41, 50, 50, 50, 50, 26, 26, 26, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 7, 40, 41, 10, 39, 8, 9, 4, 6, 5] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001455109365 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001455109365 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001455109365/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001455109365/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001455109365 Building ZINC001455109365 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001455109365' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001455109365 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455109365 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001455109365/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001455109365 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 658) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](N2C(=O)O[C@H]3CN(C(=O)OC(C)(C)C)C[C@H]32)C1) `ZINC001455109365.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455109365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001455109365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001455109365 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](N2C(=O)O[C@H]3CN(C(=O)OC(C)(C)C)C[C@H]32)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.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 12, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 4, 8, 8, 8, 8, 10, 22, 22, 22, 22, 22, 22, 22, 22, 36, 36, 50, 50, 50, 50, 22, 22, 22, 8, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 8, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 116 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001455109365 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001455109365/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001455109365 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 659) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](N2C(=O)O[C@H]3CN(C(=O)OC(C)(C)C)C[C@H]32)C1) `ZINC001455109365.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455109365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001455109365/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001455109365 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](N2C(=O)O[C@H]3CN(C(=O)OC(C)(C)C)C[C@H]32)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.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 12, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 6, 6, 6, 6, 10, 26, 26, 26, 26, 26, 26, 26, 26, 41, 41, 50, 50, 50, 50, 26, 26, 26, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 36, 37, 38, 7, 40, 41, 10, 39, 8, 9, 4, 6, 5] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001455109365 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001455109365 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001455109365/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001455109365/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001455109365 Building ZINC001456491310 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001456491310' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001456491310 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456491310 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001456491310/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001456491310 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 660) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/660 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/660' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)ccc1S(=O)(=O)N1CCCC1) `ZINC001456491310.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456491310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001456491310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001456491310 none COc1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)ccc1S(=O)(=O)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 34, 34, 34, 37, 37, 37, 37, 9, 9, 9, 9, 2, 5, 5, 5, 5, 5, 5, 5, 9, 9, 37, 37, 37, 37, 37, 37, 37, 37] 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]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001456491310 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001456491310/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001456491310 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 661) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/661 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/661' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)ccc1S(=O)(=O)N1CCCC1) `ZINC001456491310.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456491310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001456491310/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001456491310 none COc1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)ccc1S(=O)(=O)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 35, 35, 35, 38, 38, 38, 38, 9, 9, 9, 9, 2, 5, 5, 5, 5, 5, 5, 5, 9, 9, 38, 38, 38, 38, 38, 38, 38, 38] 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]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001456491310 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001456491310 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001456491310/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001456491310/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001456491310 Building ZINC001456491310 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001456491310' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001456491310 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456491310 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001456491310/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001456491310 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 660) grep: /scratch/xiaobo/418326/xbt-8058088.46/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(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)ccc1S(=O)(=O)N1CCCC1) `ZINC001456491310.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456491310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001456491310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001456491310 none COc1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)ccc1S(=O)(=O)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 34, 34, 34, 37, 37, 37, 37, 9, 9, 9, 9, 2, 5, 5, 5, 5, 5, 5, 5, 9, 9, 37, 37, 37, 37, 37, 37, 37, 37] 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]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001456491310 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001456491310/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001456491310 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 661) grep: /scratch/xiaobo/418326/xbt-8058088.46/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(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)ccc1S(=O)(=O)N1CCCC1) `ZINC001456491310.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456491310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001456491310/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001456491310 none COc1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)ccc1S(=O)(=O)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 35, 35, 35, 38, 38, 38, 38, 9, 9, 9, 9, 2, 5, 5, 5, 5, 5, 5, 5, 9, 9, 38, 38, 38, 38, 38, 38, 38, 38] 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]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001456491310 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001456491310 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001456491310/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001456491310/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001456491310 Building ZINC001457293680 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457293680' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457293680 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457293680 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457293680/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457293680 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 662) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/662 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/662' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)N(C(=O)OC(C)(C)C)CC2)cn1) `ZINC001457293680.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457293680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457293680/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001457293680 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)N(C(=O)OC(C)(C)C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 3, 3, 1, 1, 1, 2, 5, 6, 7, 7, 7, 7, 12, 12, 17, 17, 17, 17, 7, 7, 13, 13, 18, 18, 18, 18, 7, 7, 3, 3, 5, 5, 5, 5, 5, 3, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 18, 18, 18, 18, 18, 18, 18, 18, 18, 7, 7, 7, 7, 3] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457293680 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457293680/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457293680 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 663) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/663 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/663' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)N(C(=O)OC(C)(C)C)CC2)cn1) `ZINC001457293680.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457293680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457293680/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001457293680 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)N(C(=O)OC(C)(C)C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 3, 3, 1, 1, 1, 2, 4, 6, 7, 7, 7, 7, 13, 13, 17, 17, 17, 17, 7, 7, 14, 14, 19, 20, 20, 20, 7, 7, 3, 3, 5, 5, 5, 5, 5, 3, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 20, 20, 20, 20, 20, 20, 20, 20, 20, 7, 7, 7, 7, 3] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457293680 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001457293680 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457293680/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457293680/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457293680 Building ZINC001457293680 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457293680' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457293680 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457293680 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457293680/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457293680 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 662) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)N(C(=O)OC(C)(C)C)CC2)cn1) `ZINC001457293680.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457293680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457293680/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001457293680 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)N(C(=O)OC(C)(C)C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 3, 3, 1, 1, 1, 2, 5, 6, 7, 7, 7, 7, 12, 12, 17, 17, 17, 17, 7, 7, 13, 13, 18, 18, 18, 18, 7, 7, 3, 3, 5, 5, 5, 5, 5, 3, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 18, 18, 18, 18, 18, 18, 18, 18, 18, 7, 7, 7, 7, 3] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457293680 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457293680/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457293680 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 663) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)N(C(=O)OC(C)(C)C)CC2)cn1) `ZINC001457293680.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457293680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457293680/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001457293680 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)N(C(=O)OC(C)(C)C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 3, 3, 1, 1, 1, 2, 4, 6, 7, 7, 7, 7, 13, 13, 17, 17, 17, 17, 7, 7, 14, 14, 19, 20, 20, 20, 7, 7, 3, 3, 5, 5, 5, 5, 5, 3, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 20, 20, 20, 20, 20, 20, 20, 20, 20, 7, 7, 7, 7, 3] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457293680 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001457293680 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457293680/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457293680/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457293680 Building ZINC001457359440 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457359440' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457359440 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457359440 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457359440/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457359440 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 664) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/664 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/664' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(N(Cc2ccccc2)C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cc1OC) `ZINC001457359440.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457359440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457359440/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001457359440 none COc1ccc(N(Cc2ccccc2)C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cc1OC 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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', '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'] 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, 14, 8, 11, 11, 1, 8, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 6, 6, 6, 1, 1, 1, 2, 3, 3, 2, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 6, 6, 6, 14, 11, 11, 11, 6, 6, 2, 2, 3, 3, 3, 3, 3, 2, 5, 5, 2, 2, 2, 2, 6, 14, 14, 14] 50 rigid atoms, others: [5, 6, 7, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 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: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457359440 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457359440/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457359440 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 665) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/665 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/665' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(N(Cc2ccccc2)C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cc1OC) `ZINC001457359440.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457359440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457359440/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001457359440 none COc1ccc(N(Cc2ccccc2)C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cc1OC 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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', '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'] 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, 14, 8, 11, 11, 1, 8, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 6, 6, 6, 1, 1, 1, 2, 3, 3, 2, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 6, 6, 6, 14, 11, 11, 11, 6, 6, 2, 2, 3, 3, 2, 3, 3, 2, 5, 5, 2, 2, 2, 2, 6, 14, 14, 14] 50 rigid atoms, others: [5, 6, 7, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 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: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457359440 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001457359440 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457359440/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457359440/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457359440 Building ZINC001457359440 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457359440' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457359440 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457359440 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457359440/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457359440 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 664) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc(N(Cc2ccccc2)C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cc1OC) `ZINC001457359440.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457359440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457359440/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001457359440 none COc1ccc(N(Cc2ccccc2)C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cc1OC 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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', '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'] 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, 14, 8, 11, 11, 1, 8, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 6, 6, 6, 1, 1, 1, 2, 3, 3, 2, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 6, 6, 6, 14, 11, 11, 11, 6, 6, 2, 2, 3, 3, 3, 3, 3, 2, 5, 5, 2, 2, 2, 2, 6, 14, 14, 14] 50 rigid atoms, others: [5, 6, 7, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 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: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457359440 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457359440/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457359440 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 665) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc(N(Cc2ccccc2)C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cc1OC) `ZINC001457359440.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457359440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457359440/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001457359440 none COc1ccc(N(Cc2ccccc2)C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cc1OC 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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', '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'] 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, 14, 8, 11, 11, 1, 8, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 6, 6, 6, 1, 1, 1, 2, 3, 3, 2, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 6, 6, 6, 14, 11, 11, 11, 6, 6, 2, 2, 3, 3, 2, 3, 3, 2, 5, 5, 2, 2, 2, 2, 6, 14, 14, 14] 50 rigid atoms, others: [5, 6, 7, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 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: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457359440 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001457359440 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457359440/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457359440/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457359440 Building ZINC001457697674 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457697674' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457697674 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457697674 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457697674/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457697674 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 666) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/666 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/666' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCN(c2nc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)n[nH]2)CC1) `ZINC001457697674.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457697674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457697674/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001457697674 none CC(C)(C)OC(=O)N1CCN(c2nc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)n[nH]2)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', 'N.pl3', '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', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 8, 8, 6, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 35, 26, 30, 28, 12, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 30, 30, 35, 35, 35, 35, 35, 35, 35, 35, 35, 30, 30, 30, 30, 1, 3, 3, 3, 3, 30, 30, 30, 30] 50 rigid atoms, others: [16, 13, 14, 15, 48, 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, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457697674 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457697674/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457697674 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 667) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/667 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/667' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCN(c2nc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)n[nH]2)CC1) `ZINC001457697674.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457697674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457697674/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001457697674 none CC(C)(C)OC(=O)N1CCN(c2nc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)n[nH]2)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', 'N.pl3', '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', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 8, 8, 6, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 26, 34, 26, 29, 28, 12, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 29, 29, 34, 34, 34, 34, 34, 34, 34, 34, 34, 29, 29, 29, 29, 1, 3, 3, 3, 3, 29, 29, 29, 29] 50 rigid atoms, others: [16, 13, 14, 15, 48, 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, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457697674 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001457697674 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457697674/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457697674/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457697674 Building ZINC001457697674 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457697674' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457697674 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457697674 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457697674/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457697674 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 666) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC(C)(C)OC(=O)N1CCN(c2nc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)n[nH]2)CC1) `ZINC001457697674.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457697674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457697674/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001457697674 none CC(C)(C)OC(=O)N1CCN(c2nc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)n[nH]2)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', 'N.pl3', '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', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 8, 8, 6, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 35, 26, 30, 28, 12, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 30, 30, 35, 35, 35, 35, 35, 35, 35, 35, 35, 30, 30, 30, 30, 1, 3, 3, 3, 3, 30, 30, 30, 30] 50 rigid atoms, others: [16, 13, 14, 15, 48, 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, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457697674 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457697674/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457697674 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 667) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC(C)(C)OC(=O)N1CCN(c2nc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)n[nH]2)CC1) `ZINC001457697674.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457697674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457697674/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001457697674 none CC(C)(C)OC(=O)N1CCN(c2nc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)n[nH]2)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', 'N.pl3', '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', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 8, 8, 6, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 26, 34, 26, 29, 28, 12, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 29, 29, 34, 34, 34, 34, 34, 34, 34, 34, 34, 29, 29, 29, 29, 1, 3, 3, 3, 3, 29, 29, 29, 29] 50 rigid atoms, others: [16, 13, 14, 15, 48, 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, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457697674 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001457697674 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457697674/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457697674/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457697674 Building ZINC001457726633 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457726633' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457726633 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457726633 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457726633/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457726633 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 668) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/668 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/668' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1=O) `ZINC001457726633.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457726633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457726633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001457726633 none COCCN1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 11, 7, 7, 7, 7, 5, 2, 7, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 7, 7, 7, 15, 15, 15, 15, 15, 11, 11, 7, 7, 7, 7, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 7, 7] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457726633 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457726633/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457726633 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 669) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/669 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/669' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1=O) `ZINC001457726633.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457726633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457726633/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001457726633 none COCCN1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 13, 10, 7, 7, 7, 7, 5, 2, 7, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 7, 7, 7, 14, 14, 14, 13, 13, 10, 10, 7, 7, 7, 7, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 7, 7] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457726633 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001457726633 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457726633/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457726633/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457726633 Building ZINC001457726633 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457726633' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457726633 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457726633 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457726633/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457726633 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 668) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COCCN1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1=O) `ZINC001457726633.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457726633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457726633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001457726633 none COCCN1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 11, 7, 7, 7, 7, 5, 2, 7, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 7, 7, 7, 15, 15, 15, 15, 15, 11, 11, 7, 7, 7, 7, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 7, 7] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457726633 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457726633/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457726633 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 669) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COCCN1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1=O) `ZINC001457726633.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457726633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457726633/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001457726633 none COCCN1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 13, 10, 7, 7, 7, 7, 5, 2, 7, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 7, 7, 7, 14, 14, 14, 13, 13, 10, 10, 7, 7, 7, 7, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 7, 7] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457726633 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001457726633 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457726633/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457726633/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457726633 Building ZINC001457928635 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457928635' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457928635 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457928635 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457928635/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457928635 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 670) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/670 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/670' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H](C)O1) `ZINC001457928635.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457928635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457928635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001457928635 none COC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H](C)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 9, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 3, 8, 3, 3, 3, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 3, 3, 3, 3, 3, 8, 8, 8, 3, 3, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 3, 3, 3, 3, 3] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 31 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457928635 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457928635/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457928635 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 671) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/671 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/671' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H](C)O1) `ZINC001457928635.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457928635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457928635/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001457928635 none COC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H](C)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 9, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 3, 8, 3, 3, 3, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 4, 8, 8, 8, 8, 8, 8, 2, 2, 3, 3, 3, 3, 3, 8, 8, 8, 3, 3, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 3, 3, 3, 3, 3] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457928635 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001457928635 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457928635/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457928635/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457928635 Building ZINC001457928635 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457928635' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457928635 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457928635 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457928635/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457928635 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 670) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H](C)O1) `ZINC001457928635.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457928635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457928635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001457928635 none COC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H](C)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 9, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 3, 8, 3, 3, 3, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 3, 3, 3, 3, 3, 8, 8, 8, 3, 3, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 3, 3, 3, 3, 3] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 31 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457928635 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457928635/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457928635 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 671) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H](C)O1) `ZINC001457928635.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457928635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457928635/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001457928635 none COC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H](C)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 9, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 3, 8, 3, 3, 3, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 4, 8, 8, 8, 8, 8, 8, 2, 2, 3, 3, 3, 3, 3, 8, 8, 8, 3, 3, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 3, 3, 3, 3, 3] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457928635 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001457928635 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457928635/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457928635/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457928635 Building ZINC001457934903 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457934903' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457934903 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457934903 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457934903/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457934903 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 672) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/672 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/672' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@@H]2[C@H](C1)OC(=O)N2C1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1) `ZINC001457934903.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457934903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457934903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001457934903 none CC(C)(C)OC(=O)N1C[C@@H]2[C@H](C1)OC(=O)N2C1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)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.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 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, 3, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 37, 22, 37, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 22, 4, 4, 4, 4, 4, 1, 1, 2, 1, 1, 4, 4, 4, 4] 100 rigid atoms, others: [32, 54, 56, 53, 22, 57, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 55, 58, 59, 60, 61]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457934903 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457934903/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457934903 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 673) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/673 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/673' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@@H]2[C@H](C1)OC(=O)N2C1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1) `ZINC001457934903.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457934903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457934903/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001457934903 none CC(C)(C)OC(=O)N1C[C@@H]2[C@H](C1)OC(=O)N2C1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)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.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 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, 3, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 34, 22, 34, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 22, 4, 4, 4, 4, 4, 1, 1, 2, 1, 1, 4, 4, 4, 4] 100 rigid atoms, others: [32, 54, 56, 53, 22, 57, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 55, 58, 59, 60, 61]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457934903 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001457934903 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457934903/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457934903/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457934903 Building ZINC001457934903 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457934903' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457934903 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457934903 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457934903/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457934903 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 672) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC(C)(C)OC(=O)N1C[C@@H]2[C@H](C1)OC(=O)N2C1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1) `ZINC001457934903.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457934903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457934903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001457934903 none CC(C)(C)OC(=O)N1C[C@@H]2[C@H](C1)OC(=O)N2C1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)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.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 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, 3, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 37, 22, 37, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 22, 4, 4, 4, 4, 4, 1, 1, 2, 1, 1, 4, 4, 4, 4] 100 rigid atoms, others: [32, 54, 56, 53, 22, 57, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 55, 58, 59, 60, 61]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457934903 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457934903/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457934903 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 673) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC(C)(C)OC(=O)N1C[C@@H]2[C@H](C1)OC(=O)N2C1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1) `ZINC001457934903.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457934903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457934903/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001457934903 none CC(C)(C)OC(=O)N1C[C@@H]2[C@H](C1)OC(=O)N2C1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)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.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 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, 3, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 34, 22, 34, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 22, 4, 4, 4, 4, 4, 1, 1, 2, 1, 1, 4, 4, 4, 4] 100 rigid atoms, others: [32, 54, 56, 53, 22, 57, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 55, 58, 59, 60, 61]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457934903 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001457934903 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457934903/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457934903/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001457934903 Building ZINC001458014941 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458014941' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458014941 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458014941 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458014941/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458014941 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 674) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/674 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/674' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccccc1CS(=O)(=O)N1CCCC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001458014941.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458014941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458014941/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001458014941 none O=C(NCc1ccccc1CS(=O)(=O)N1CCCC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 14, 11, 11, 8, 5, 5, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 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, 7, 7, 7] 0 hydrogens need 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, 11, 11, 8, 11, 11, 11, 12, 19, 19, 19, 31, 31, 31, 31, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 8, 8, 11, 11, 9, 11, 12, 12, 31, 31, 31, 31, 31, 31, 31, 31, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458014941 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458014941/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458014941 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 675) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/675 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/675' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccccc1CS(=O)(=O)N1CCCC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001458014941.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458014941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458014941/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001458014941 none O=C(NCc1ccccc1CS(=O)(=O)N1CCCC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 14, 11, 11, 8, 5, 5, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 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, 7, 7, 7] 0 hydrogens need 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, 12, 12, 11, 12, 12, 12, 12, 19, 19, 19, 28, 28, 28, 28, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 8, 8, 12, 12, 8, 12, 12, 12, 28, 28, 28, 28, 28, 28, 28, 28, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458014941 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001458014941 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458014941/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458014941/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458014941 Building ZINC001458014941 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458014941' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458014941 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458014941 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458014941/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458014941 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 674) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: O=C(NCc1ccccc1CS(=O)(=O)N1CCCC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001458014941.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458014941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458014941/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001458014941 none O=C(NCc1ccccc1CS(=O)(=O)N1CCCC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 14, 11, 11, 8, 5, 5, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 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, 7, 7, 7] 0 hydrogens need 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, 11, 11, 8, 11, 11, 11, 12, 19, 19, 19, 31, 31, 31, 31, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 8, 8, 11, 11, 9, 11, 12, 12, 31, 31, 31, 31, 31, 31, 31, 31, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458014941 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458014941/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458014941 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 675) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: O=C(NCc1ccccc1CS(=O)(=O)N1CCCC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001458014941.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458014941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458014941/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001458014941 none O=C(NCc1ccccc1CS(=O)(=O)N1CCCC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 14, 11, 11, 8, 5, 5, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 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, 7, 7, 7] 0 hydrogens need 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, 12, 12, 11, 12, 12, 12, 12, 19, 19, 19, 28, 28, 28, 28, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 8, 8, 12, 12, 8, 12, 12, 12, 28, 28, 28, 28, 28, 28, 28, 28, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458014941 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001458014941 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458014941/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458014941/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458014941 Building ZINC001458029342 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458029342' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458029342 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458029342 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458029342/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458029342 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 676) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/676 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/676' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)[C@H](CS(N)(=O)=O)C1) `ZINC001458029342.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458029342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458029342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001458029342 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)[C@H](CS(N)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 14, 8, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 6, 11, 11, 11, 4, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 4, 4, 4, 4, 4, 6, 6, 11, 11, 4, 4] 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]) total number of confs: 68 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458029342 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458029342/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458029342 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 677) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/677 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/677' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)[C@H](CS(N)(=O)=O)C1) `ZINC001458029342.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458029342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458029342/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001458029342 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)[C@H](CS(N)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 14, 8, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 11, 11, 3, 11, 11, 11, 11, 11, 11, 2, 2, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 6, 10, 10, 10, 4, 2, 2, 2, 11, 11, 8, 11, 2, 2, 2, 4, 4, 4, 4, 4, 6, 6, 10, 10, 4, 4] 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]) total number of confs: 75 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458029342 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001458029342 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458029342/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458029342/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458029342 Building ZINC001458029342 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458029342' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458029342 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458029342 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458029342/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458029342 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 676) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/676: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)[C@H](CS(N)(=O)=O)C1) `ZINC001458029342.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458029342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458029342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001458029342 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)[C@H](CS(N)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 14, 8, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 6, 11, 11, 11, 4, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 4, 4, 4, 4, 4, 6, 6, 11, 11, 4, 4] 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]) total number of confs: 68 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458029342 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458029342/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458029342 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 677) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/677: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)[C@H](CS(N)(=O)=O)C1) `ZINC001458029342.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458029342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458029342/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001458029342 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)[C@H](CS(N)(=O)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 14, 8, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 11, 11, 3, 11, 11, 11, 11, 11, 11, 2, 2, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 6, 10, 10, 10, 4, 2, 2, 2, 11, 11, 8, 11, 2, 2, 2, 4, 4, 4, 4, 4, 6, 6, 10, 10, 4, 4] 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]) total number of confs: 75 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458029342 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001458029342 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458029342/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458029342/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458029342 Building ZINC001458422155 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458422155' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458422155 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458422155 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458422155/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458422155 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 678) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/678 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/678' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(S(=O)(=O)NCCNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c(C)s1) `ZINC001458422155.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458422155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458422155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001458422155 none Cc1cc(S(=O)(=O)NCCNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c(C)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.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, 1, 1, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 5, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 29, 45, 45, 15, 11, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 45, 45, 45, 45, 45, 45, 45, 29, 15, 15, 11, 11, 2, 4, 4, 45, 45, 45] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458422155 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458422155/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458422155 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 679) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/679 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/679' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(S(=O)(=O)NCCNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c(C)s1) `ZINC001458422155.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458422155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458422155/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001458422155 none Cc1cc(S(=O)(=O)NCCNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c(C)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.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, 1, 1, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 5, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 46, 30, 46, 46, 15, 11, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 46, 46, 46, 46, 46, 46, 46, 30, 15, 15, 11, 11, 2, 4, 4, 46, 46, 46] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458422155 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001458422155 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458422155/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458422155/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458422155 Building ZINC001458422155 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458422155' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458422155 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458422155 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458422155/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458422155 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 678) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1cc(S(=O)(=O)NCCNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c(C)s1) `ZINC001458422155.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458422155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458422155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001458422155 none Cc1cc(S(=O)(=O)NCCNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c(C)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.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, 1, 1, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 5, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 29, 45, 45, 15, 11, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 45, 45, 45, 45, 45, 45, 45, 29, 15, 15, 11, 11, 2, 4, 4, 45, 45, 45] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458422155 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458422155/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458422155 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 679) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1cc(S(=O)(=O)NCCNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c(C)s1) `ZINC001458422155.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458422155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458422155/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001458422155 none Cc1cc(S(=O)(=O)NCCNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c(C)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.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, 1, 1, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 5, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 46, 30, 46, 46, 15, 11, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 46, 46, 46, 46, 46, 46, 46, 30, 15, 15, 11, 11, 2, 4, 4, 46, 46, 46] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458422155 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001458422155 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458422155/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458422155/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001458422155 Building ZINC001459589213 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459589213' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459589213 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459589213 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459589213/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459589213 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 680) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/680 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/680' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(c2cccc(CN(C)C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)c2)S(=O)(=O)C1) `ZINC001459589213.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459589213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459589213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001459589213 none C[C@H]1CN(c2cccc(CN(C)C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)c2)S(=O)(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 14, 14, 14, 14, 8, 3, 2, 3, 1, 2, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 14, 39, 39, 39, 39, 39, 39, 39, 39, 39, 14, 14, 14, 8, 8, 3, 3, 3, 6, 7, 7, 6, 7, 7, 6, 14, 39, 39] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459589213 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459589213/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459589213 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 681) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/681 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/681' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(c2cccc(CN(C)C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)c2)S(=O)(=O)C1) `ZINC001459589213.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459589213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459589213/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001459589213 none C[C@H]1CN(c2cccc(CN(C)C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)c2)S(=O)(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 13, 13, 13, 13, 8, 3, 2, 3, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 38, 38, 38, 38, 38, 38, 38, 38, 38, 13, 13, 13, 8, 8, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 13, 38, 38] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459589213 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001459589213 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459589213/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459589213/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459589213 Building ZINC001459589213 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459589213' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459589213 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459589213 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459589213/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459589213 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 680) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: C[C@H]1CN(c2cccc(CN(C)C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)c2)S(=O)(=O)C1) `ZINC001459589213.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459589213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459589213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001459589213 none C[C@H]1CN(c2cccc(CN(C)C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)c2)S(=O)(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 14, 14, 14, 14, 8, 3, 2, 3, 1, 2, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 14, 39, 39, 39, 39, 39, 39, 39, 39, 39, 14, 14, 14, 8, 8, 3, 3, 3, 6, 7, 7, 6, 7, 7, 6, 14, 39, 39] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459589213 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459589213/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459589213 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 681) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: C[C@H]1CN(c2cccc(CN(C)C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)c2)S(=O)(=O)C1) `ZINC001459589213.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459589213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459589213/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001459589213 none C[C@H]1CN(c2cccc(CN(C)C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)c2)S(=O)(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 13, 13, 13, 13, 8, 3, 2, 3, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 38, 38, 38, 38, 38, 38, 38, 38, 38, 13, 13, 13, 8, 8, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 13, 38, 38] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459589213 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001459589213 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459589213/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459589213/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459589213 Building ZINC001459589216 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459589216' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459589216 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459589216 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459589216/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459589216 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 682) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/682 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/682' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(c2cccc(CN(C)C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)c2)S(=O)(=O)C1) `ZINC001459589216.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459589216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459589216/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001459589216 none C[C@@H]1CN(c2cccc(CN(C)C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)c2)S(=O)(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 14, 8, 3, 2, 3, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 38, 38, 38, 38, 38, 38, 38, 38, 38, 14, 14, 14, 8, 8, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 14, 38, 38] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459589216 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459589216/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459589216 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 683) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/683 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/683' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(c2cccc(CN(C)C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)c2)S(=O)(=O)C1) `ZINC001459589216.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459589216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459589216/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001459589216 none C[C@@H]1CN(c2cccc(CN(C)C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)c2)S(=O)(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 14, 14, 14, 14, 8, 3, 2, 3, 1, 2, 1, 1, 1, 5, 5, 5, 5, 6, 6, 5, 6, 6, 5, 14, 40, 40, 40, 40, 40, 40, 40, 40, 40, 14, 14, 14, 8, 8, 3, 3, 3, 5, 6, 6, 5, 6, 6, 5, 14, 40, 40] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459589216 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001459589216 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459589216/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459589216/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459589216 Building ZINC001459589216 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459589216' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459589216 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459589216 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459589216/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459589216 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 682) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: C[C@@H]1CN(c2cccc(CN(C)C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)c2)S(=O)(=O)C1) `ZINC001459589216.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459589216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459589216/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001459589216 none C[C@@H]1CN(c2cccc(CN(C)C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)c2)S(=O)(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 14, 8, 3, 2, 3, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 38, 38, 38, 38, 38, 38, 38, 38, 38, 14, 14, 14, 8, 8, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 14, 38, 38] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459589216 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459589216/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459589216 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 683) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: C[C@@H]1CN(c2cccc(CN(C)C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)c2)S(=O)(=O)C1) `ZINC001459589216.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459589216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459589216/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001459589216 none C[C@@H]1CN(c2cccc(CN(C)C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)c2)S(=O)(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 14, 14, 14, 14, 8, 3, 2, 3, 1, 2, 1, 1, 1, 5, 5, 5, 5, 6, 6, 5, 6, 6, 5, 14, 40, 40, 40, 40, 40, 40, 40, 40, 40, 14, 14, 14, 8, 8, 3, 3, 3, 5, 6, 6, 5, 6, 6, 5, 14, 40, 40] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459589216 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001459589216 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459589216/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459589216/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459589216 Building ZINC001459887549 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459887549' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459887549 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459887549 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459887549/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459887549 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 684) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/684 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/684' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(Br)c(S(=O)(=O)NCCNC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)c1) `ZINC001459887549.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459887549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459887549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001459887549 none Cc1ccc(Br)c(S(=O)(=O)NCCNC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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, 17, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 50, 50, 50, 50, 50, 36, 50, 50, 21, 16, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 36, 21, 21, 16, 16, 3, 2, 2, 2, 2, 2, 2, 50] 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: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459887549 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459887549/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459887549 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 685) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/685 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/685' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(Br)c(S(=O)(=O)NCCNC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)c1) `ZINC001459887549.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459887549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459887549/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001459887549 none Cc1ccc(Br)c(S(=O)(=O)NCCNC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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, 17, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 37, 50, 50, 22, 17, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 37, 22, 22, 17, 17, 3, 2, 2, 2, 2, 2, 2, 50] 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: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459887549 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001459887549 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459887549/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459887549/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459887549 Building ZINC001459887549 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459887549' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459887549 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459887549 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459887549/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459887549 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 684) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1ccc(Br)c(S(=O)(=O)NCCNC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)c1) `ZINC001459887549.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459887549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459887549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001459887549 none Cc1ccc(Br)c(S(=O)(=O)NCCNC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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, 17, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 50, 50, 50, 50, 50, 36, 50, 50, 21, 16, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 36, 21, 21, 16, 16, 3, 2, 2, 2, 2, 2, 2, 50] 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: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459887549 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459887549/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459887549 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 685) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1ccc(Br)c(S(=O)(=O)NCCNC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)c1) `ZINC001459887549.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459887549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459887549/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001459887549 none Cc1ccc(Br)c(S(=O)(=O)NCCNC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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, 17, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 37, 50, 50, 22, 17, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 37, 22, 22, 17, 17, 3, 2, 2, 2, 2, 2, 2, 50] 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: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459887549 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001459887549 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459887549/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459887549/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001459887549 Building ZINC001462256775 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462256775' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462256775 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462256775 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462256775/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462256775 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 686) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/686 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/686' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CC(=O)OC)c2cccc(I)c2)cn1) `ZINC001462256775.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462256775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462256775/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001462256775 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CC(=O)OC)c2cccc(I)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 12, 5, 1, 1, 1, 1, 1, 18, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 7, 7, 7, 3, 10, 10, 6, 10, 10, 10, 6, 6, 13, 13, 13, 13, 13, 6, 3, 3, 3, 7, 7, 7, 10, 10, 6, 10, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462256775 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462256775/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462256775 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 687) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/687 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/687' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](CC(=O)OC)c2cccc(I)c2)cn1) `ZINC001462256775.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462256775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462256775/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001462256775 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](CC(=O)OC)c2cccc(I)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 12, 5, 1, 1, 1, 1, 1, 18, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 8, 8, 8, 4, 10, 10, 8, 10, 10, 10, 5, 5, 11, 11, 11, 11, 11, 5, 4, 4, 4, 8, 8, 8, 10, 10, 8, 10, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/418326/xbt-8058088.46/working/building/ZINC001462256775 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001462256775 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462256775/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462256775/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462256775 Building ZINC001462256775 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462256775' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462256775 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462256775 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462256775/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462256775 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 686) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CC(=O)OC)c2cccc(I)c2)cn1) `ZINC001462256775.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462256775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462256775/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001462256775 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CC(=O)OC)c2cccc(I)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 12, 5, 1, 1, 1, 1, 1, 18, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 7, 7, 7, 3, 10, 10, 6, 10, 10, 10, 6, 6, 13, 13, 13, 13, 13, 6, 3, 3, 3, 7, 7, 7, 10, 10, 6, 10, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462256775 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462256775/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462256775 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 687) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](CC(=O)OC)c2cccc(I)c2)cn1) `ZINC001462256775.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462256775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462256775/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001462256775 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](CC(=O)OC)c2cccc(I)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 12, 5, 1, 1, 1, 1, 1, 18, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 8, 8, 8, 4, 10, 10, 8, 10, 10, 10, 5, 5, 11, 11, 11, 11, 11, 5, 4, 4, 4, 8, 8, 8, 10, 10, 8, 10, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/418326/xbt-8058088.46/working/building/ZINC001462256775 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001462256775 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462256775/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462256775/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462256775 Building ZINC001462703155 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462703155' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462703155 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462703155 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462703155/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462703155 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 688) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/688 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/688' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc(CS(=O)(=O)N(C)C)cc1) `ZINC001462703155.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462703155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462703155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001462703155 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc(CS(=O)(=O)N(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 14, 11, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 2, 13, 26, 26, 13, 13, 35, 49, 49, 49, 49, 49, 26, 26, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 2, 13, 13, 26, 26, 35, 35, 49, 49, 49, 49, 49, 49, 26, 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, 53, 54, 55, 56, 57]) total number of confs: 281 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462703155 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462703155/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462703155 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 689) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/689 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/689' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc(CS(=O)(=O)N(C)C)cc1) `ZINC001462703155.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462703155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462703155/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001462703155 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc(CS(=O)(=O)N(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 14, 11, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 12, 25, 25, 12, 12, 33, 48, 48, 48, 49, 49, 25, 25, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 12, 12, 25, 25, 33, 33, 49, 49, 49, 49, 49, 49, 25, 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, 55, 56, 57]) total number of confs: 290 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462703155 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001462703155 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462703155/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462703155/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462703155 Building ZINC001462703155 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462703155' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462703155 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462703155 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462703155/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462703155 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 688) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/688: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc(CS(=O)(=O)N(C)C)cc1) `ZINC001462703155.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462703155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462703155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001462703155 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc(CS(=O)(=O)N(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 14, 11, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 2, 13, 26, 26, 13, 13, 35, 49, 49, 49, 49, 49, 26, 26, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 2, 13, 13, 26, 26, 35, 35, 49, 49, 49, 49, 49, 49, 26, 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, 53, 54, 55, 56, 57]) total number of confs: 281 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462703155 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462703155/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462703155 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 689) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/689: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc(CS(=O)(=O)N(C)C)cc1) `ZINC001462703155.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462703155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462703155/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001462703155 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc(CS(=O)(=O)N(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 14, 11, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 12, 25, 25, 12, 12, 33, 48, 48, 48, 49, 49, 25, 25, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 12, 12, 25, 25, 33, 33, 49, 49, 49, 49, 49, 49, 25, 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, 55, 56, 57]) total number of confs: 290 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462703155 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001462703155 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462703155/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462703155/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462703155 Building ZINC001462759864 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462759864' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462759864 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462759864 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462759864/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462759864 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 690) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/690 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/690' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@]12C[C@@H](NC(=O)OC(C)(C)C)C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c1cnn(c3ccccc3)c1)C2) `ZINC001462759864.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462759864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462759864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001462759864 none COC(=O)[C@@]12C[C@@H](NC(=O)OC(C)(C)C)C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c1cnn(c3ccccc3)c1)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', '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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 20, 9, 9, 9, 9, 9, 22, 25, 25, 25, 25, 25, 25, 9, 9, 9, 9, 2, 1, 5, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 20, 20, 20, 9, 9, 22, 25, 25, 25, 25, 25, 25, 25, 25, 25, 9, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3, 9, 9] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462759864 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462759864/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462759864 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 691) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/691 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/691' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@]12C[C@@H](NC(=O)OC(C)(C)C)C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c1cnn(c3ccccc3)c1)C2) `ZINC001462759864.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462759864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462759864/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001462759864 none COC(=O)[C@@]12C[C@@H](NC(=O)OC(C)(C)C)C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c1cnn(c3ccccc3)c1)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', '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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 18, 8, 8, 8, 8, 8, 23, 25, 25, 26, 26, 26, 26, 8, 8, 8, 8, 2, 1, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 8, 18, 18, 18, 8, 8, 23, 26, 26, 26, 26, 26, 26, 26, 26, 26, 8, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 8, 8] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462759864 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001462759864 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462759864/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462759864/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462759864 Building ZINC001462759864 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462759864' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462759864 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462759864 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462759864/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462759864 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 690) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COC(=O)[C@@]12C[C@@H](NC(=O)OC(C)(C)C)C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c1cnn(c3ccccc3)c1)C2) `ZINC001462759864.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462759864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462759864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001462759864 none COC(=O)[C@@]12C[C@@H](NC(=O)OC(C)(C)C)C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c1cnn(c3ccccc3)c1)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', '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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 20, 9, 9, 9, 9, 9, 22, 25, 25, 25, 25, 25, 25, 9, 9, 9, 9, 2, 1, 5, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 20, 20, 20, 9, 9, 22, 25, 25, 25, 25, 25, 25, 25, 25, 25, 9, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3, 9, 9] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462759864 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462759864/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462759864 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 691) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COC(=O)[C@@]12C[C@@H](NC(=O)OC(C)(C)C)C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c1cnn(c3ccccc3)c1)C2) `ZINC001462759864.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462759864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462759864/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001462759864 none COC(=O)[C@@]12C[C@@H](NC(=O)OC(C)(C)C)C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c1cnn(c3ccccc3)c1)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', '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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 18, 8, 8, 8, 8, 8, 23, 25, 25, 26, 26, 26, 26, 8, 8, 8, 8, 2, 1, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 8, 18, 18, 18, 8, 8, 23, 26, 26, 26, 26, 26, 26, 26, 26, 26, 8, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 8, 8] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462759864 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001462759864 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462759864/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462759864/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001462759864 Building ZINC001463548084 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463548084' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463548084 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463548084 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463548084/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463548084 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 692) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/692 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/692' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(S(=O)(=O)c2c(F)cccc2F)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001463548084.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463548084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463548084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001463548084 none O=C(N1CCN(S(=O)(=O)c2c(F)cccc2F)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 14, 11, 11, 1, 1, 15, 1, 1, 1, 1, 15, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 11, 11, 11, 11, 24, 24, 24, 31, 31, 31, 31, 31, 31, 31, 11, 11, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 11, 31, 31, 31, 11, 11, 11, 11, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463548084 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463548084/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463548084 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 693) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/693 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/693' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(S(=O)(=O)c2c(F)cccc2F)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001463548084.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463548084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463548084/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001463548084 none O=C(N1CCN(S(=O)(=O)c2c(F)cccc2F)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 14, 11, 11, 1, 1, 15, 1, 1, 1, 1, 15, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 8, 16, 16, 16, 16, 27, 27, 27, 31, 31, 31, 31, 31, 31, 31, 16, 16, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16, 31, 31, 31, 16, 16, 16, 16, 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]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463548084 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001463548084 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463548084/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463548084/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463548084 Building ZINC001463548084 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463548084' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463548084 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463548084 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463548084/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463548084 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 692) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: O=C(N1CCN(S(=O)(=O)c2c(F)cccc2F)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001463548084.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463548084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463548084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001463548084 none O=C(N1CCN(S(=O)(=O)c2c(F)cccc2F)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 14, 11, 11, 1, 1, 15, 1, 1, 1, 1, 15, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 11, 11, 11, 11, 24, 24, 24, 31, 31, 31, 31, 31, 31, 31, 11, 11, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 11, 31, 31, 31, 11, 11, 11, 11, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463548084 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463548084/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463548084 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 693) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: O=C(N1CCN(S(=O)(=O)c2c(F)cccc2F)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001463548084.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463548084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463548084/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001463548084 none O=C(N1CCN(S(=O)(=O)c2c(F)cccc2F)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 14, 11, 11, 1, 1, 15, 1, 1, 1, 1, 15, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 8, 16, 16, 16, 16, 27, 27, 27, 31, 31, 31, 31, 31, 31, 31, 16, 16, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16, 31, 31, 31, 16, 16, 16, 16, 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]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463548084 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001463548084 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463548084/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463548084/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463548084 Building ZINC001463700855 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463700855' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463700855 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463700855 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463700855/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463700855 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 694) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/694 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/694' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Br)c(C(F)(F)F)c1) `ZINC001463700855.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463700855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463700855/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001463700855 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Br)c(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 17, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 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, 13, 13, 13, 4, 1, 1, 1, 1, 3, 3, 3, 10, 10, 5, 10, 10, 10, 10, 10, 10, 10, 4, 4, 4, 4, 13, 13, 4, 3, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463700855 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463700855/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463700855 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 695) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/695 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/695' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(Br)c(C(F)(F)F)c1) `ZINC001463700855.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463700855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463700855/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001463700855 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(Br)c(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 17, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 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, 13, 13, 13, 4, 1, 1, 1, 1, 3, 3, 3, 10, 10, 8, 9, 10, 10, 10, 10, 10, 10, 4, 4, 4, 4, 13, 13, 4, 3, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463700855 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001463700855 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463700855/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463700855/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463700855 Building ZINC001463700855 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463700855' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463700855 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463700855 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463700855/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463700855 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 694) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Br)c(C(F)(F)F)c1) `ZINC001463700855.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463700855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463700855/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001463700855 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Br)c(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 17, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 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, 13, 13, 13, 4, 1, 1, 1, 1, 3, 3, 3, 10, 10, 5, 10, 10, 10, 10, 10, 10, 10, 4, 4, 4, 4, 13, 13, 4, 3, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463700855 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463700855/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463700855 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 695) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(Br)c(C(F)(F)F)c1) `ZINC001463700855.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463700855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463700855/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001463700855 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(Br)c(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 17, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 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, 13, 13, 13, 4, 1, 1, 1, 1, 3, 3, 3, 10, 10, 8, 9, 10, 10, 10, 10, 10, 10, 4, 4, 4, 4, 13, 13, 4, 3, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463700855 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001463700855 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463700855/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463700855/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463700855 Building ZINC001463932025 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463932025' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463932025 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463932025 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463932025/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463932025 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 696) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/696 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/696' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1c[nH]c2ccccc21)c1ccccc1) `ZINC001463932025.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463932025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463932025/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001463932025 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1c[nH]c2ccccc21)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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', '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, 8, 1, 1, 14, 8, 11, 11, 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, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 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, 5, 2, 1, 1, 1, 1, 3, 3, 3, 15, 23, 23, 28, 28, 28, 28, 28, 28, 28, 28, 28, 23, 25, 25, 23, 25, 25, 2, 2, 2, 2, 5, 5, 2, 3, 15, 15, 28, 28, 28, 28, 28, 25, 25, 23, 25, 25] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 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: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463932025 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463932025/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463932025 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 697) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/697 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/697' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H](c1c[nH]c2ccccc21)c1ccccc1) `ZINC001463932025.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463932025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463932025/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001463932025 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H](c1c[nH]c2ccccc21)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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', '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, 8, 1, 1, 14, 8, 11, 11, 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, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 1, 1, 2, 2, 2, 11, 17, 17, 25, 25, 25, 25, 25, 25, 25, 25, 25, 17, 22, 22, 17, 22, 22, 1, 1, 1, 1, 4, 4, 1, 2, 11, 11, 25, 25, 25, 25, 25, 22, 22, 17, 22, 22] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 8, 9, 10, 11, 12, 2, 40, 3, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463932025 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001463932025 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463932025/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463932025/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463932025 Building ZINC001463932025 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463932025' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463932025 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463932025 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463932025/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463932025 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 696) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1c[nH]c2ccccc21)c1ccccc1) `ZINC001463932025.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463932025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463932025/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001463932025 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](c1c[nH]c2ccccc21)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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', '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, 8, 1, 1, 14, 8, 11, 11, 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, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 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, 5, 2, 1, 1, 1, 1, 3, 3, 3, 15, 23, 23, 28, 28, 28, 28, 28, 28, 28, 28, 28, 23, 25, 25, 23, 25, 25, 2, 2, 2, 2, 5, 5, 2, 3, 15, 15, 28, 28, 28, 28, 28, 25, 25, 23, 25, 25] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 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: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463932025 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463932025/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463932025 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 697) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H](c1c[nH]c2ccccc21)c1ccccc1) `ZINC001463932025.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463932025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463932025/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001463932025 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H](c1c[nH]c2ccccc21)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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', '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, 8, 1, 1, 14, 8, 11, 11, 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, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 1, 1, 2, 2, 2, 11, 17, 17, 25, 25, 25, 25, 25, 25, 25, 25, 25, 17, 22, 22, 17, 22, 22, 1, 1, 1, 1, 4, 4, 1, 2, 11, 11, 25, 25, 25, 25, 25, 22, 22, 17, 22, 22] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 8, 9, 10, 11, 12, 2, 40, 3, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463932025 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001463932025 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463932025/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463932025/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463932025 Building ZINC001463932026 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463932026' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463932026 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463932026 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463932026/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463932026 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 698) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/698 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/698' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H](c1c[nH]c2ccccc21)c1ccccc1) `ZINC001463932026.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463932026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463932026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001463932026 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H](c1c[nH]c2ccccc21)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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', '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, 8, 1, 1, 14, 8, 11, 11, 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, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 1, 1, 3, 3, 3, 12, 18, 18, 26, 26, 26, 26, 26, 26, 26, 26, 26, 18, 23, 23, 18, 23, 23, 1, 1, 1, 1, 4, 4, 1, 3, 12, 12, 26, 26, 26, 26, 26, 23, 23, 18, 23, 23] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 8, 9, 10, 11, 12, 2, 40, 3, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 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/418326/xbt-8058088.46/working/building/ZINC001463932026 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463932026/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463932026 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 699) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/699 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/699' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@H](c1c[nH]c2ccccc21)c1ccccc1) `ZINC001463932026.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463932026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463932026/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001463932026 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@H](c1c[nH]c2ccccc21)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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', '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, 8, 1, 1, 14, 8, 11, 11, 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, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 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, 5, 2, 1, 1, 1, 1, 3, 3, 3, 15, 23, 23, 28, 28, 28, 28, 28, 28, 28, 28, 28, 23, 25, 25, 23, 25, 25, 2, 2, 2, 2, 5, 5, 2, 3, 15, 15, 28, 28, 28, 28, 28, 25, 25, 23, 25, 25] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 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: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463932026 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001463932026 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463932026/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463932026/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463932026 Building ZINC001463932026 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463932026' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463932026 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463932026 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463932026/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463932026 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 698) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H](c1c[nH]c2ccccc21)c1ccccc1) `ZINC001463932026.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463932026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463932026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001463932026 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H](c1c[nH]c2ccccc21)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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', '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, 8, 1, 1, 14, 8, 11, 11, 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, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 1, 1, 3, 3, 3, 12, 18, 18, 26, 26, 26, 26, 26, 26, 26, 26, 26, 18, 23, 23, 18, 23, 23, 1, 1, 1, 1, 4, 4, 1, 3, 12, 12, 26, 26, 26, 26, 26, 23, 23, 18, 23, 23] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 8, 9, 10, 11, 12, 2, 40, 3, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 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/418326/xbt-8058088.46/working/building/ZINC001463932026 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463932026/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463932026 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 699) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@H](c1c[nH]c2ccccc21)c1ccccc1) `ZINC001463932026.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463932026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463932026/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001463932026 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@H](c1c[nH]c2ccccc21)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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', '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, 8, 1, 1, 14, 8, 11, 11, 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, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 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, 5, 2, 1, 1, 1, 1, 3, 3, 3, 15, 23, 23, 28, 28, 28, 28, 28, 28, 28, 28, 28, 23, 25, 25, 23, 25, 25, 2, 2, 2, 2, 5, 5, 2, 3, 15, 15, 28, 28, 28, 28, 28, 25, 25, 23, 25, 25] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 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: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463932026 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001463932026 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463932026/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463932026/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463932026 Building ZINC001463943083 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463943083' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463943083 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463943083 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463943083/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463943083 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 700) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/700 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/700' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)c1ccc(S(=O)(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)CC2)cc1) `ZINC001463943083.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463943083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463943083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001463943083 none CC(=O)c1ccc(S(=O)(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 14, 38, 14, 34, 34, 14, 9, 14, 14, 9, 9, 9, 3, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 34, 34, 38, 38, 38, 34, 34, 9, 9, 9, 9, 5, 5, 5, 5, 9, 9, 9, 9, 34, 34] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463943083 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463943083/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463943083 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 701) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/701 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/701' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)c1ccc(S(=O)(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)CC2)cc1) `ZINC001463943083.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463943083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463943083/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001463943083 none CC(=O)c1ccc(S(=O)(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 16, 38, 16, 35, 35, 16, 10, 16, 16, 10, 10, 10, 3, 1, 5, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 35, 35, 38, 38, 38, 35, 35, 10, 10, 10, 10, 3, 3, 3, 3, 10, 10, 10, 10, 35, 35] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463943083 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001463943083 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463943083/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463943083/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463943083 Building ZINC001463943083 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463943083' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463943083 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463943083 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463943083/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463943083 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 700) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC(=O)c1ccc(S(=O)(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)CC2)cc1) `ZINC001463943083.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463943083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463943083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001463943083 none CC(=O)c1ccc(S(=O)(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 14, 38, 14, 34, 34, 14, 9, 14, 14, 9, 9, 9, 3, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 34, 34, 38, 38, 38, 34, 34, 9, 9, 9, 9, 5, 5, 5, 5, 9, 9, 9, 9, 34, 34] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463943083 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463943083/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463943083 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 701) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC(=O)c1ccc(S(=O)(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)CC2)cc1) `ZINC001463943083.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463943083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463943083/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001463943083 none CC(=O)c1ccc(S(=O)(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 16, 38, 16, 35, 35, 16, 10, 16, 16, 10, 10, 10, 3, 1, 5, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 35, 35, 38, 38, 38, 35, 35, 10, 10, 10, 10, 3, 3, 3, 3, 10, 10, 10, 10, 35, 35] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463943083 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001463943083 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463943083/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463943083/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001463943083 Building ZINC001464280380 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464280380' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464280380 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464280380 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464280380/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464280380 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 702) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/702 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/702' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)ccc1OCCC(C)C) `ZINC001464280380.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464280380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464280380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001464280380 none COc1cc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)ccc1OCCC(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.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 7, 7, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 7, 7, 7, 7, 21, 29, 44, 44, 44, 11, 11, 11, 7, 3, 3, 3, 2, 1, 3, 3, 1, 1, 1, 1, 7, 7, 29, 29, 44, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [45, 43, 40, 9, 11, 12, 13, 14, 15, 16, 20, 21, 22, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464280380 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464280380/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464280380 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 703) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/703 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/703' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)ccc1OCCC(C)C) `ZINC001464280380.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464280380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464280380/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001464280380 none COc1cc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)ccc1OCCC(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.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 6, 6, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 6, 6, 6, 6, 22, 23, 39, 39, 39, 12, 12, 12, 6, 4, 4, 4, 2, 1, 3, 3, 1, 1, 1, 1, 6, 6, 23, 23, 39, 39, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [45, 43, 40, 9, 11, 12, 13, 14, 15, 16, 20, 21, 22, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464280380 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001464280380 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464280380/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464280380/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464280380 Building ZINC001464280380 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464280380' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464280380 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464280380 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464280380/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464280380 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 702) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)ccc1OCCC(C)C) `ZINC001464280380.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464280380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464280380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001464280380 none COc1cc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)ccc1OCCC(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.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 7, 7, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 7, 7, 7, 7, 21, 29, 44, 44, 44, 11, 11, 11, 7, 3, 3, 3, 2, 1, 3, 3, 1, 1, 1, 1, 7, 7, 29, 29, 44, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [45, 43, 40, 9, 11, 12, 13, 14, 15, 16, 20, 21, 22, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464280380 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464280380/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464280380 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 703) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)ccc1OCCC(C)C) `ZINC001464280380.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464280380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464280380/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001464280380 none COc1cc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)ccc1OCCC(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.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 6, 6, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 6, 6, 6, 6, 22, 23, 39, 39, 39, 12, 12, 12, 6, 4, 4, 4, 2, 1, 3, 3, 1, 1, 1, 1, 6, 6, 23, 23, 39, 39, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [45, 43, 40, 9, 11, 12, 13, 14, 15, 16, 20, 21, 22, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464280380 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001464280380 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464280380/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464280380/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464280380 Building ZINC001464280384 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464280384' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464280384 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464280384 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464280384/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464280384 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 704) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/704 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/704' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)ccc1OCCC(C)C) `ZINC001464280384.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464280384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464280384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001464280384 none COc1cc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)ccc1OCCC(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.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 6, 6, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 6, 6, 6, 6, 22, 22, 39, 39, 39, 11, 11, 11, 6, 4, 4, 4, 2, 1, 3, 3, 1, 1, 1, 1, 6, 6, 22, 22, 39, 39, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [45, 43, 40, 9, 11, 12, 13, 14, 15, 16, 20, 21, 22, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464280384 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464280384/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464280384 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 705) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/705 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/705' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)ccc1OCCC(C)C) `ZINC001464280384.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464280384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464280384/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001464280384 none COc1cc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)ccc1OCCC(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.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 7, 7, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 7, 7, 7, 7, 26, 30, 43, 43, 43, 11, 11, 11, 7, 3, 3, 3, 2, 1, 3, 3, 1, 1, 1, 1, 7, 7, 30, 30, 43, 43, 43, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [45, 43, 40, 9, 11, 12, 13, 14, 15, 16, 20, 21, 22, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464280384 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001464280384 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464280384/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464280384/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464280384 Building ZINC001464280384 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464280384' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464280384 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464280384 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464280384/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464280384 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 704) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)ccc1OCCC(C)C) `ZINC001464280384.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464280384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464280384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001464280384 none COc1cc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)ccc1OCCC(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.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 6, 6, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 6, 6, 6, 6, 22, 22, 39, 39, 39, 11, 11, 11, 6, 4, 4, 4, 2, 1, 3, 3, 1, 1, 1, 1, 6, 6, 22, 22, 39, 39, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [45, 43, 40, 9, 11, 12, 13, 14, 15, 16, 20, 21, 22, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464280384 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464280384/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464280384 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 705) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)ccc1OCCC(C)C) `ZINC001464280384.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464280384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464280384/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001464280384 none COc1cc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)ccc1OCCC(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.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 7, 7, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 7, 7, 7, 7, 26, 30, 43, 43, 43, 11, 11, 11, 7, 3, 3, 3, 2, 1, 3, 3, 1, 1, 1, 1, 7, 7, 30, 30, 43, 43, 43, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [45, 43, 40, 9, 11, 12, 13, 14, 15, 16, 20, 21, 22, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464280384 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001464280384 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464280384/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464280384/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464280384 Building ZINC001464817451 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464817451' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464817451 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464817451 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464817451/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464817451 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 706) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/706 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/706' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccc(OCc2ccc(F)cc2)cc1) `ZINC001464817451.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464817451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464817451/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001464817451 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccc(OCc2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 6, 7, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 6, 3, 1, 3, 1, 1, 1, 3, 3, 3, 6, 6, 6, 3, 3, 3, 6, 11, 11, 6, 6, 19, 19, 27, 27, 22, 27, 27, 27, 11, 11, 6, 6, 6, 3, 3, 6, 6, 3, 3, 3, 3, 11, 11, 19, 19, 27, 27, 27, 27, 11, 11] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 111 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464817451 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464817451/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464817451 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 707) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/707 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/707' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccc(OCc2ccc(F)cc2)cc1) `ZINC001464817451.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464817451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464817451/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001464817451 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccc(OCc2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 6, 7, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 5, 3, 1, 3, 1, 1, 1, 3, 3, 3, 6, 6, 6, 3, 3, 3, 5, 10, 10, 5, 5, 17, 17, 19, 19, 17, 19, 19, 19, 10, 10, 5, 5, 5, 3, 3, 6, 6, 3, 3, 3, 3, 10, 10, 17, 17, 19, 19, 19, 19, 10, 10] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 84 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464817451 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001464817451 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464817451/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464817451/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464817451 Building ZINC001464817451 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464817451' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464817451 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464817451 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464817451/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464817451 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 706) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccc(OCc2ccc(F)cc2)cc1) `ZINC001464817451.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464817451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464817451/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001464817451 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccc(OCc2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 6, 7, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 6, 3, 1, 3, 1, 1, 1, 3, 3, 3, 6, 6, 6, 3, 3, 3, 6, 11, 11, 6, 6, 19, 19, 27, 27, 22, 27, 27, 27, 11, 11, 6, 6, 6, 3, 3, 6, 6, 3, 3, 3, 3, 11, 11, 19, 19, 27, 27, 27, 27, 11, 11] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 111 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464817451 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464817451/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464817451 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 707) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccc(OCc2ccc(F)cc2)cc1) `ZINC001464817451.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464817451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464817451/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001464817451 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccc(OCc2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 6, 7, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 5, 3, 1, 3, 1, 1, 1, 3, 3, 3, 6, 6, 6, 3, 3, 3, 5, 10, 10, 5, 5, 17, 17, 19, 19, 17, 19, 19, 19, 10, 10, 5, 5, 5, 3, 3, 6, 6, 3, 3, 3, 3, 10, 10, 17, 17, 19, 19, 19, 19, 10, 10] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 84 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464817451 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001464817451 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464817451/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464817451/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464817451 Building ZINC001464817453 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464817453' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464817453 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464817453 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464817453/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464817453 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 708) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/708 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/708' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccc(OCc2ccc(F)cc2)cc1) `ZINC001464817453.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464817453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464817453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001464817453 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccc(OCc2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 6, 7, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 5, 3, 1, 3, 1, 1, 1, 3, 3, 3, 6, 6, 6, 3, 3, 3, 5, 9, 9, 5, 8, 16, 16, 18, 18, 17, 18, 18, 18, 9, 9, 5, 5, 5, 3, 3, 6, 6, 3, 3, 3, 3, 9, 9, 16, 16, 18, 18, 18, 18, 9, 9] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 81 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464817453 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464817453/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464817453 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 709) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/709 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/709' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccc(OCc2ccc(F)cc2)cc1) `ZINC001464817453.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464817453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464817453/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001464817453 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccc(OCc2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 6, 7, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 6, 3, 1, 3, 1, 1, 1, 3, 3, 3, 6, 6, 6, 3, 3, 3, 6, 11, 11, 6, 9, 19, 19, 27, 27, 19, 27, 27, 27, 11, 11, 6, 6, 6, 3, 3, 6, 6, 3, 3, 3, 3, 11, 11, 19, 19, 27, 27, 27, 27, 11, 11] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 131 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464817453 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001464817453 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464817453/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464817453/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464817453 Building ZINC001464817453 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464817453' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464817453 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464817453 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464817453/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464817453 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 708) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccc(OCc2ccc(F)cc2)cc1) `ZINC001464817453.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464817453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464817453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001464817453 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccc(OCc2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 6, 7, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 5, 3, 1, 3, 1, 1, 1, 3, 3, 3, 6, 6, 6, 3, 3, 3, 5, 9, 9, 5, 8, 16, 16, 18, 18, 17, 18, 18, 18, 9, 9, 5, 5, 5, 3, 3, 6, 6, 3, 3, 3, 3, 9, 9, 16, 16, 18, 18, 18, 18, 9, 9] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 81 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464817453 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464817453/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464817453 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 709) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccc(OCc2ccc(F)cc2)cc1) `ZINC001464817453.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464817453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464817453/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001464817453 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)c1ccc(OCc2ccc(F)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 7, 7, 7, 6, 7, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 6, 3, 1, 3, 1, 1, 1, 3, 3, 3, 6, 6, 6, 3, 3, 3, 6, 11, 11, 6, 9, 19, 19, 27, 27, 19, 27, 27, 27, 11, 11, 6, 6, 6, 3, 3, 6, 6, 3, 3, 3, 3, 11, 11, 19, 19, 27, 27, 27, 27, 11, 11] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 131 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464817453 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001464817453 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464817453/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464817453/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464817453 Building ZINC001464948341 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464948341' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464948341 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464948341 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464948341/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464948341 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 710) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/710 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/710' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2ccc(F)cc2)sc1[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001464948341.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464948341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464948341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001464948341 none Cc1nc(c2ccc(F)cc2)sc1[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 14, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 21, 21, 21, 21, 21, 21, 14, 6, 3, 6, 6, 3, 1, 3, 1, 1, 1, 3, 3, 3, 7, 7, 7, 3, 3, 3, 14, 14, 14, 21, 21, 21, 21, 6, 6, 6, 3, 3, 7, 7, 3, 3, 3, 3] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464948341 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464948341/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464948341 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 711) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/711 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/711' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2ccc(F)cc2)sc1[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001464948341.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464948341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464948341/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001464948341 none Cc1nc(c2ccc(F)cc2)sc1[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 14, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 17, 17, 17, 17, 17, 17, 14, 6, 4, 6, 6, 4, 1, 4, 1, 1, 1, 4, 4, 4, 14, 14, 14, 4, 4, 4, 14, 14, 14, 17, 17, 17, 17, 6, 6, 6, 4, 4, 14, 14, 4, 4, 4, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464948341 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001464948341 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464948341/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464948341/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464948341 Building ZINC001464948341 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464948341' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464948341 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464948341 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464948341/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464948341 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 710) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1nc(c2ccc(F)cc2)sc1[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001464948341.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464948341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464948341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001464948341 none Cc1nc(c2ccc(F)cc2)sc1[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 14, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 21, 21, 21, 21, 21, 21, 14, 6, 3, 6, 6, 3, 1, 3, 1, 1, 1, 3, 3, 3, 7, 7, 7, 3, 3, 3, 14, 14, 14, 21, 21, 21, 21, 6, 6, 6, 3, 3, 7, 7, 3, 3, 3, 3] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464948341 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464948341/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464948341 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 711) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1nc(c2ccc(F)cc2)sc1[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001464948341.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464948341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464948341/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001464948341 none Cc1nc(c2ccc(F)cc2)sc1[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 14, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 17, 17, 17, 17, 17, 17, 14, 6, 4, 6, 6, 4, 1, 4, 1, 1, 1, 4, 4, 4, 14, 14, 14, 4, 4, 4, 14, 14, 14, 17, 17, 17, 17, 6, 6, 6, 4, 4, 14, 14, 4, 4, 4, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464948341 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001464948341 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464948341/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464948341/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464948341 Building ZINC001464948347 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464948347' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464948347 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464948347 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464948347/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464948347 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 712) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/712 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/712' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2ccc(F)cc2)sc1[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001464948347.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464948347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464948347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001464948347 none Cc1nc(c2ccc(F)cc2)sc1[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 14, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 17, 17, 16, 16, 17, 17, 13, 5, 3, 5, 5, 3, 1, 3, 1, 1, 1, 4, 4, 4, 14, 14, 14, 4, 4, 4, 13, 13, 13, 17, 17, 17, 17, 5, 5, 5, 3, 4, 14, 14, 4, 4, 4, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464948347 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464948347/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464948347 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 713) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/713 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/713' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2ccc(F)cc2)sc1[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001464948347.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464948347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464948347/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001464948347 none Cc1nc(c2ccc(F)cc2)sc1[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 14, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 21, 21, 19, 21, 21, 21, 14, 6, 3, 6, 6, 3, 1, 3, 1, 1, 1, 3, 3, 3, 7, 7, 7, 3, 3, 3, 14, 14, 14, 21, 21, 21, 21, 6, 6, 6, 3, 3, 7, 7, 3, 3, 3, 3] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464948347 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001464948347 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464948347/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464948347/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464948347 Building ZINC001464948347 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464948347' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464948347 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464948347 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464948347/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464948347 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 712) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1nc(c2ccc(F)cc2)sc1[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001464948347.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464948347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464948347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001464948347 none Cc1nc(c2ccc(F)cc2)sc1[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 14, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 17, 17, 16, 16, 17, 17, 13, 5, 3, 5, 5, 3, 1, 3, 1, 1, 1, 4, 4, 4, 14, 14, 14, 4, 4, 4, 13, 13, 13, 17, 17, 17, 17, 5, 5, 5, 3, 4, 14, 14, 4, 4, 4, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464948347 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464948347/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464948347 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 713) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1nc(c2ccc(F)cc2)sc1[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001464948347.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464948347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464948347/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001464948347 none Cc1nc(c2ccc(F)cc2)sc1[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 14, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 21, 21, 19, 21, 21, 21, 14, 6, 3, 6, 6, 3, 1, 3, 1, 1, 1, 3, 3, 3, 7, 7, 7, 3, 3, 3, 14, 14, 14, 21, 21, 21, 21, 6, 6, 6, 3, 3, 7, 7, 3, 3, 3, 3] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464948347 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001464948347 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464948347/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464948347/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464948347 Building ZINC001464950991 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464950991' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464950991 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464950991 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464950991/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464950991 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 714) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/714 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/714' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(=O)NCCN2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)CC2)cc1) `ZINC001464950991.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464950991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464950991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001464950991 none COc1ccc(C(=O)NCCN2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 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, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 21, 35, 35, 21, 21, 21, 13, 11, 6, 6, 6, 6, 3, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 35, 35, 35, 35, 35, 35, 35, 21, 13, 13, 11, 11, 6, 6, 6, 6, 4, 4, 4, 4, 6, 6, 6, 6, 35, 35] 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]) total number of confs: 164 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464950991 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464950991/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464950991 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 715) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/715 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/715' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(=O)NCCN2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)CC2)cc1) `ZINC001464950991.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464950991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464950991/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001464950991 none COc1ccc(C(=O)NCCN2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 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, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 37, 23, 40, 40, 23, 23, 23, 12, 10, 5, 5, 5, 5, 3, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 40, 40, 40, 40, 40, 40, 40, 23, 12, 12, 10, 10, 5, 5, 5, 5, 3, 3, 3, 3, 5, 5, 5, 5, 40, 40] 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]) total number of confs: 193 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464950991 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001464950991 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464950991/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464950991/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464950991 Building ZINC001464950991 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464950991' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464950991 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464950991 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464950991/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464950991 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 714) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc(C(=O)NCCN2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)CC2)cc1) `ZINC001464950991.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464950991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464950991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001464950991 none COc1ccc(C(=O)NCCN2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 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, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 21, 35, 35, 21, 21, 21, 13, 11, 6, 6, 6, 6, 3, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 35, 35, 35, 35, 35, 35, 35, 21, 13, 13, 11, 11, 6, 6, 6, 6, 4, 4, 4, 4, 6, 6, 6, 6, 35, 35] 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]) total number of confs: 164 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464950991 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464950991/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464950991 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 715) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc(C(=O)NCCN2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)CC2)cc1) `ZINC001464950991.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464950991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464950991/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001464950991 none COc1ccc(C(=O)NCCN2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 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, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 37, 23, 40, 40, 23, 23, 23, 12, 10, 5, 5, 5, 5, 3, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 40, 40, 40, 40, 40, 40, 40, 23, 12, 12, 10, 10, 5, 5, 5, 5, 3, 3, 3, 3, 5, 5, 5, 5, 40, 40] 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]) total number of confs: 193 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464950991 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001464950991 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464950991/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464950991/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464950991 Building ZINC001464957653 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464957653' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464957653 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464957653 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464957653/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464957653 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 716) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/716 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/716' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ccc([C@@H](c2cccnc2)N(CC)C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cc1) `ZINC001464957653.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464957653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464957653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001464957653 none CCc1ccc([C@@H](c2cccnc2)N(CC)C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 1, 1, 1, 1, 8, 1, 8, 5, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 9, 9, 5, 2, 5, 5, 14, 14, 14, 14, 14, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 14, 14, 14, 14, 2, 2, 2, 2, 2, 1, 4, 4, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [54, 49, 55, 17, 19, 20, 21, 22, 23, 24, 52, 28, 29, 30, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 56, 57]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464957653 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464957653/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464957653 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 717) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/717 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/717' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ccc([C@@H](c2cccnc2)N(CC)C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cc1) `ZINC001464957653.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464957653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464957653/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001464957653 none CCc1ccc([C@@H](c2cccnc2)N(CC)C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 1, 1, 1, 1, 8, 1, 8, 5, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 10, 10, 5, 2, 5, 5, 17, 17, 17, 17, 17, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 17, 17, 17, 17, 2, 2, 2, 2, 2, 1, 4, 4, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [54, 49, 55, 17, 19, 20, 21, 22, 23, 24, 52, 28, 29, 30, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 56, 57]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464957653 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001464957653 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464957653/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464957653/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464957653 Building ZINC001464957653 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464957653' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464957653 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464957653 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464957653/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464957653 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 716) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCc1ccc([C@@H](c2cccnc2)N(CC)C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cc1) `ZINC001464957653.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464957653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464957653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001464957653 none CCc1ccc([C@@H](c2cccnc2)N(CC)C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 1, 1, 1, 1, 8, 1, 8, 5, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 9, 9, 5, 2, 5, 5, 14, 14, 14, 14, 14, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 14, 14, 14, 14, 2, 2, 2, 2, 2, 1, 4, 4, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [54, 49, 55, 17, 19, 20, 21, 22, 23, 24, 52, 28, 29, 30, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 56, 57]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464957653 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464957653/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464957653 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 717) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCc1ccc([C@@H](c2cccnc2)N(CC)C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cc1) `ZINC001464957653.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464957653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464957653/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001464957653 none CCc1ccc([C@@H](c2cccnc2)N(CC)C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 1, 1, 1, 1, 8, 1, 8, 5, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 10, 10, 5, 2, 5, 5, 17, 17, 17, 17, 17, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 17, 17, 17, 17, 2, 2, 2, 2, 2, 1, 4, 4, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [54, 49, 55, 17, 19, 20, 21, 22, 23, 24, 52, 28, 29, 30, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 56, 57]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464957653 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001464957653 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464957653/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464957653/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464957653 Building ZINC001464957660 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464957660' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464957660 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464957660 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464957660/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464957660 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 718) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/718 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/718' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ccc([C@H](c2cccnc2)N(CC)C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cc1) `ZINC001464957660.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464957660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464957660/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001464957660 none CCc1ccc([C@H](c2cccnc2)N(CC)C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 1, 1, 1, 1, 8, 1, 8, 5, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 5, 2, 5, 5, 16, 16, 16, 16, 16, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 16, 16, 16, 16, 2, 2, 2, 2, 2, 1, 4, 4, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [54, 49, 55, 17, 19, 20, 21, 22, 23, 24, 52, 28, 29, 30, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 56, 57]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464957660 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464957660/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464957660 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 719) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/719 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/719' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ccc([C@H](c2cccnc2)N(CC)C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cc1) `ZINC001464957660.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464957660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464957660/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001464957660 none CCc1ccc([C@H](c2cccnc2)N(CC)C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 1, 1, 1, 1, 8, 1, 8, 5, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 9, 9, 5, 2, 5, 5, 14, 14, 14, 14, 14, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 14, 14, 14, 14, 2, 2, 2, 2, 2, 1, 4, 4, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [54, 49, 55, 17, 19, 20, 21, 22, 23, 24, 52, 28, 29, 30, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 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/418326/xbt-8058088.46/working/building/ZINC001464957660 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001464957660 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464957660/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464957660/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464957660 Building ZINC001464957660 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464957660' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464957660 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464957660 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464957660/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464957660 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 718) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCc1ccc([C@H](c2cccnc2)N(CC)C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cc1) `ZINC001464957660.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464957660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464957660/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001464957660 none CCc1ccc([C@H](c2cccnc2)N(CC)C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 1, 1, 1, 1, 8, 1, 8, 5, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 5, 2, 5, 5, 16, 16, 16, 16, 16, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 16, 16, 16, 16, 2, 2, 2, 2, 2, 1, 4, 4, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [54, 49, 55, 17, 19, 20, 21, 22, 23, 24, 52, 28, 29, 30, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 56, 57]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464957660 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464957660/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464957660 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 719) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCc1ccc([C@H](c2cccnc2)N(CC)C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cc1) `ZINC001464957660.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464957660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464957660/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001464957660 none CCc1ccc([C@H](c2cccnc2)N(CC)C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 1, 1, 1, 1, 8, 1, 8, 5, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 9, 9, 5, 2, 5, 5, 14, 14, 14, 14, 14, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 14, 14, 14, 14, 2, 2, 2, 2, 2, 1, 4, 4, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [54, 49, 55, 17, 19, 20, 21, 22, 23, 24, 52, 28, 29, 30, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 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/418326/xbt-8058088.46/working/building/ZINC001464957660 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001464957660 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464957660/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464957660/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001464957660 Building ZINC001465275365 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465275365' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465275365 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001465275365 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465275365/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465275365 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 720) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/720 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/720' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)Cc1cccc(Br)c1) `ZINC001465275365.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001465275365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465275365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001465275365 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)Cc1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 11, 16, 27, 27, 27, 27, 27, 27, 14, 14, 14, 14, 14, 11, 11, 2, 1, 4, 4, 1, 1, 1, 1, 16, 16, 27, 27, 27, 27] 50 rigid atoms, others: [36, 6, 39, 8, 9, 10, 11, 12, 13, 17, 18, 19, 41, 40, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 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/418326/xbt-8058088.46/working/building/ZINC001465275365 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465275365/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465275365 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 721) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/721 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/721' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)Cc1cccc(Br)c1) `ZINC001465275365.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001465275365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465275365/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001465275365 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)Cc1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 11, 15, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 14, 17, 31, 31, 31, 31, 31, 31, 15, 15, 15, 15, 15, 11, 11, 2, 2, 5, 5, 2, 2, 2, 2, 17, 17, 31, 31, 31, 31] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 116 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465275365 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001465275365 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465275365/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465275365/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465275365 Building ZINC001465275365 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465275365' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465275365 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001465275365 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465275365/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465275365 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 720) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)Cc1cccc(Br)c1) `ZINC001465275365.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001465275365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465275365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001465275365 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)Cc1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 11, 16, 27, 27, 27, 27, 27, 27, 14, 14, 14, 14, 14, 11, 11, 2, 1, 4, 4, 1, 1, 1, 1, 16, 16, 27, 27, 27, 27] 50 rigid atoms, others: [36, 6, 39, 8, 9, 10, 11, 12, 13, 17, 18, 19, 41, 40, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 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/418326/xbt-8058088.46/working/building/ZINC001465275365 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465275365/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465275365 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 721) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)Cc1cccc(Br)c1) `ZINC001465275365.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001465275365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465275365/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001465275365 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)Cc1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 11, 15, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 14, 17, 31, 31, 31, 31, 31, 31, 15, 15, 15, 15, 15, 11, 11, 2, 2, 5, 5, 2, 2, 2, 2, 17, 17, 31, 31, 31, 31] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 116 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465275365 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001465275365 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465275365/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465275365/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465275365 Building ZINC001465275366 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465275366' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465275366 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001465275366 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465275366/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465275366 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 722) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/722 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/722' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)Cc1cccc(Br)c1) `ZINC001465275366.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001465275366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465275366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001465275366 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)Cc1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 11, 15, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 14, 17, 31, 31, 31, 31, 31, 31, 15, 15, 15, 15, 15, 11, 11, 2, 2, 5, 5, 2, 2, 2, 2, 17, 17, 31, 31, 31, 31] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 116 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465275366 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465275366/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465275366 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 723) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/723 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/723' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)Cc1cccc(Br)c1) `ZINC001465275366.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001465275366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465275366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001465275366 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)Cc1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 11, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 12, 17, 28, 28, 28, 28, 28, 28, 15, 15, 15, 15, 15, 11, 11, 2, 1, 4, 4, 1, 1, 1, 1, 17, 17, 28, 28, 28, 28] 50 rigid atoms, others: [36, 6, 39, 8, 9, 10, 11, 12, 13, 17, 18, 19, 41, 40, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 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/418326/xbt-8058088.46/working/building/ZINC001465275366 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001465275366 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465275366/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465275366/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465275366 Building ZINC001465275366 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465275366' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465275366 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001465275366 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465275366/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465275366 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 722) grep: /scratch/xiaobo/418326/xbt-8058088.46/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@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)Cc1cccc(Br)c1) `ZINC001465275366.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001465275366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465275366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001465275366 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)Cc1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 11, 15, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 14, 17, 31, 31, 31, 31, 31, 31, 15, 15, 15, 15, 15, 11, 11, 2, 2, 5, 5, 2, 2, 2, 2, 17, 17, 31, 31, 31, 31] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 116 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465275366 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465275366/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465275366 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 723) grep: /scratch/xiaobo/418326/xbt-8058088.46/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@H](CNC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)Cc1cccc(Br)c1) `ZINC001465275366.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001465275366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465275366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001465275366 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)Cc1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 11, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 12, 17, 28, 28, 28, 28, 28, 28, 15, 15, 15, 15, 15, 11, 11, 2, 1, 4, 4, 1, 1, 1, 1, 17, 17, 28, 28, 28, 28] 50 rigid atoms, others: [36, 6, 39, 8, 9, 10, 11, 12, 13, 17, 18, 19, 41, 40, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 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/418326/xbt-8058088.46/working/building/ZINC001465275366 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001465275366 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465275366/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465275366/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465275366 Building ZINC001465483317 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465483317' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465483317 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001465483317 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465483317/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465483317 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 724) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/724 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/724' -> `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)CCNS(=O)(=O)c1ccc(C)cc1) `ZINC001465483317.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001465483317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465483317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001465483317 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)CCNS(=O)(=O)c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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'] 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, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 4, 5, 5, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 4, 5, 19, 32, 32, 32, 32, 32, 32, 32, 32, 32, 2, 2, 2, 5, 5, 4, 5, 5, 2, 2, 2, 2, 2, 2, 4, 4, 5, 5, 19, 32, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 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: 134 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465483317 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465483317/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465483317 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 725) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/725 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/725' -> `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)CCNS(=O)(=O)c1ccc(C)cc1) `ZINC001465483317.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001465483317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465483317/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001465483317 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)CCNS(=O)(=O)c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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'] 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, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 4, 5, 18, 30, 30, 30, 30, 30, 30, 30, 30, 30, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 2, 2, 4, 4, 5, 5, 18, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 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/418326/xbt-8058088.46/working/building/ZINC001465483317 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001465483317 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465483317/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465483317/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465483317 Building ZINC001465483317 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465483317' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465483317 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001465483317 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465483317/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465483317 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 724) grep: /scratch/xiaobo/418326/xbt-8058088.46/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(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)CCNS(=O)(=O)c1ccc(C)cc1) `ZINC001465483317.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001465483317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465483317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001465483317 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)CCNS(=O)(=O)c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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'] 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, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 4, 5, 5, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 4, 5, 19, 32, 32, 32, 32, 32, 32, 32, 32, 32, 2, 2, 2, 5, 5, 4, 5, 5, 2, 2, 2, 2, 2, 2, 4, 4, 5, 5, 19, 32, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 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: 134 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465483317 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465483317/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465483317 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 725) grep: /scratch/xiaobo/418326/xbt-8058088.46/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(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)CCNS(=O)(=O)c1ccc(C)cc1) `ZINC001465483317.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001465483317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465483317/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001465483317 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)CCNS(=O)(=O)c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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'] 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, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 4, 5, 18, 30, 30, 30, 30, 30, 30, 30, 30, 30, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 2, 2, 4, 4, 5, 5, 18, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 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/418326/xbt-8058088.46/working/building/ZINC001465483317 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001465483317 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465483317/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465483317/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465483317 Building ZINC001465735756 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465735756' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465735756 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001465735756 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465735756/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465735756 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 726) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/726 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/726' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCCOc1c(Cl)cc(Cl)cc1Cl) `ZINC001465735756.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001465735756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465735756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001465735756 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCCOc1c(Cl)cc(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 16, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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, 7, 7] 0 hydrogens need rotated 50 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, 5, 2, 1, 1, 1, 1, 2, 2, 2, 11, 15, 23, 23, 23, 23, 23, 23, 23, 23, 23, 2, 2, 2, 2, 5, 5, 2, 2, 11, 11, 15, 15, 23, 23] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465735756 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465735756/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465735756 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 727) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/727 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/727' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCCOc1c(Cl)cc(Cl)cc1Cl) `ZINC001465735756.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001465735756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465735756/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001465735756 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCCOc1c(Cl)cc(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 16, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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, 7, 7] 0 hydrogens need rotated 50 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, 5, 2, 1, 1, 1, 1, 2, 2, 2, 11, 15, 23, 23, 23, 23, 23, 23, 23, 23, 23, 2, 2, 2, 2, 5, 5, 2, 2, 11, 11, 15, 15, 23, 23] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465735756 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001465735756 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465735756/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465735756/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465735756 Building ZINC001465735756 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465735756' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465735756 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001465735756 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465735756/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465735756 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 726) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCCOc1c(Cl)cc(Cl)cc1Cl) `ZINC001465735756.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001465735756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465735756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001465735756 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCCOc1c(Cl)cc(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 16, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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, 7, 7] 0 hydrogens need rotated 50 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, 5, 2, 1, 1, 1, 1, 2, 2, 2, 11, 15, 23, 23, 23, 23, 23, 23, 23, 23, 23, 2, 2, 2, 2, 5, 5, 2, 2, 11, 11, 15, 15, 23, 23] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465735756 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465735756/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465735756 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 727) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCCOc1c(Cl)cc(Cl)cc1Cl) `ZINC001465735756.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001465735756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465735756/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001465735756 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCCOc1c(Cl)cc(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 16, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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, 7, 7] 0 hydrogens need rotated 50 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, 5, 2, 1, 1, 1, 1, 2, 2, 2, 11, 15, 23, 23, 23, 23, 23, 23, 23, 23, 23, 2, 2, 2, 2, 5, 5, 2, 2, 11, 11, 15, 15, 23, 23] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465735756 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001465735756 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465735756/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465735756/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001465735756 Building ZINC001467547494 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467547494' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467547494 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001467547494 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467547494/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467547494 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 728) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/728 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/728' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc([C@@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)ccc1Br) `ZINC001467547494.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001467547494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467547494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001467547494 none Cc1cc([C@@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', '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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 5, 1, 5, 1, 1, 1, 3, 3, 3, 7, 7, 7, 3, 3, 3, 23, 23, 17, 23, 23, 23, 23, 23, 8, 8, 8, 8, 8, 8, 3, 7, 7, 3, 3, 3, 3, 23, 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, 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/418326/xbt-8058088.46/working/building/ZINC001467547494 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467547494/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467547494 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 729) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/729 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/729' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc([C@@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)ccc1Br) `ZINC001467547494.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001467547494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467547494/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001467547494 none Cc1cc([C@@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', '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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 5, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 2, 2, 2, 7, 7, 7, 2, 2, 2, 13, 13, 9, 13, 13, 13, 13, 13, 5, 5, 5, 5, 5, 5, 2, 7, 7, 2, 2, 2, 2, 13, 13] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467547494 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001467547494 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467547494/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467547494/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467547494 Building ZINC001467547494 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467547494' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467547494 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001467547494 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467547494/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467547494 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 728) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1cc([C@@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)ccc1Br) `ZINC001467547494.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001467547494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467547494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001467547494 none Cc1cc([C@@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', '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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 5, 1, 5, 1, 1, 1, 3, 3, 3, 7, 7, 7, 3, 3, 3, 23, 23, 17, 23, 23, 23, 23, 23, 8, 8, 8, 8, 8, 8, 3, 7, 7, 3, 3, 3, 3, 23, 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, 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/418326/xbt-8058088.46/working/building/ZINC001467547494 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467547494/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467547494 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 729) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1cc([C@@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)ccc1Br) `ZINC001467547494.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001467547494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467547494/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001467547494 none Cc1cc([C@@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', '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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 5, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 2, 2, 2, 7, 7, 7, 2, 2, 2, 13, 13, 9, 13, 13, 13, 13, 13, 5, 5, 5, 5, 5, 5, 2, 7, 7, 2, 2, 2, 2, 13, 13] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467547494 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001467547494 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467547494/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467547494/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467547494 Building ZINC001467547495 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467547495' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467547495 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001467547495 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467547495/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467547495 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 730) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/730 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/730' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc([C@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)ccc1Br) `ZINC001467547495.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001467547495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467547495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001467547495 none Cc1cc([C@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', '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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 4, 4, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 3, 3, 3, 9, 9, 9, 3, 3, 3, 14, 14, 4, 4, 14, 14, 14, 14, 4, 4, 4, 4, 4, 4, 3, 9, 9, 3, 3, 3, 3, 14, 14] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467547495 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467547495/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467547495 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 731) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/731 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/731' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc([C@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)ccc1Br) `ZINC001467547495.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001467547495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467547495/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001467547495 none Cc1cc([C@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', '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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 5, 1, 5, 1, 1, 1, 3, 3, 3, 9, 9, 9, 3, 3, 3, 22, 22, 17, 22, 22, 22, 22, 22, 8, 8, 8, 8, 8, 8, 3, 9, 9, 3, 3, 3, 3, 22, 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, 44, 45, 46]) total number of confs: 82 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467547495 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001467547495 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467547495/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467547495/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467547495 Building ZINC001467547495 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467547495' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467547495 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001467547495 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467547495/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467547495 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 730) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1cc([C@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)ccc1Br) `ZINC001467547495.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001467547495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467547495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001467547495 none Cc1cc([C@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', '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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 4, 4, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 3, 3, 3, 9, 9, 9, 3, 3, 3, 14, 14, 4, 4, 14, 14, 14, 14, 4, 4, 4, 4, 4, 4, 3, 9, 9, 3, 3, 3, 3, 14, 14] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467547495 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467547495/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467547495 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 731) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1cc([C@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)ccc1Br) `ZINC001467547495.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001467547495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467547495/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001467547495 none Cc1cc([C@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', '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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 5, 1, 5, 1, 1, 1, 3, 3, 3, 9, 9, 9, 3, 3, 3, 22, 22, 17, 22, 22, 22, 22, 22, 8, 8, 8, 8, 8, 8, 3, 9, 9, 3, 3, 3, 3, 22, 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, 44, 45, 46]) total number of confs: 82 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467547495 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001467547495 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467547495/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467547495/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467547495 Building ZINC001467619498 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467619498' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467619498 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001467619498 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467619498/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467619498 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 732) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/732 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/732' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(OCC(F)F)c(C(F)(F)F)c1) `ZINC001467619498.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001467619498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467619498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001467619498 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(OCC(F)F)c(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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.3', 'F', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 5, 15, 15, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 4, 8, 16, 29, 29, 29, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 3, 3, 1, 2, 8, 8, 29, 29, 29, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 8, 9, 10, 11, 12, 36, 30, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467619498 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467619498/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467619498 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 733) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/733 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/733' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(OCC(F)F)c(C(F)(F)F)c1) `ZINC001467619498.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001467619498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467619498/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001467619498 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(OCC(F)F)c(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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.3', 'F', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 5, 15, 15, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 16, 28, 28, 28, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 3, 3, 1, 2, 8, 8, 28, 28, 28, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 8, 9, 10, 11, 12, 36, 30, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467619498 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001467619498 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467619498/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467619498/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467619498 Building ZINC001467619498 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467619498' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467619498 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001467619498 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467619498/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467619498 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 732) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/732: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(OCC(F)F)c(C(F)(F)F)c1) `ZINC001467619498.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001467619498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467619498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001467619498 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(OCC(F)F)c(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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.3', 'F', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 5, 15, 15, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 4, 8, 16, 29, 29, 29, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 3, 3, 1, 2, 8, 8, 29, 29, 29, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 8, 9, 10, 11, 12, 36, 30, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467619498 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467619498/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467619498 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 733) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/733: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(OCC(F)F)c(C(F)(F)F)c1) `ZINC001467619498.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001467619498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467619498/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001467619498 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(OCC(F)F)c(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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.3', 'F', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 5, 15, 15, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 16, 28, 28, 28, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 3, 3, 1, 2, 8, 8, 28, 28, 28, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 8, 9, 10, 11, 12, 36, 30, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467619498 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001467619498 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467619498/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467619498/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001467619498 Building ZINC001468671012 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468671012' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468671012 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468671012 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468671012/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468671012 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 734) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/734 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/734' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(S(=O)(=O)N=S2(=O)CCN(C(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)CC2)cc1) `ZINC001468671012.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468671012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468671012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001468671012 none Cc1ccc(S(=O)(=O)N=S2(=O)CCN(C(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'S.o', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 14, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 10, 50, 50, 10, 10, 10, 10, 10, 6, 2, 7, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 10, 10, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 50, 50] 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: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468671012 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468671012/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468671012 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 735) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/735 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/735' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(S(=O)(=O)N=S2(=O)CCN(C(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)CC2)cc1) `ZINC001468671012.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468671012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468671012/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001468671012 none Cc1ccc(S(=O)(=O)N=S2(=O)CCN(C(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'S.o', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 14, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 13, 50, 50, 13, 13, 13, 13, 13, 6, 2, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 48, 49, 50]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468671012 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001468671012 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468671012/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468671012/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468671012 Building ZINC001468671012 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468671012' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468671012 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468671012 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468671012/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468671012 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 734) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1ccc(S(=O)(=O)N=S2(=O)CCN(C(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)CC2)cc1) `ZINC001468671012.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468671012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468671012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001468671012 none Cc1ccc(S(=O)(=O)N=S2(=O)CCN(C(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'S.o', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 14, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 10, 50, 50, 10, 10, 10, 10, 10, 6, 2, 7, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 10, 10, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 50, 50] 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: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468671012 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468671012/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468671012 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 735) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1ccc(S(=O)(=O)N=S2(=O)CCN(C(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)CC2)cc1) `ZINC001468671012.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468671012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468671012/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001468671012 none Cc1ccc(S(=O)(=O)N=S2(=O)CCN(C(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'S.o', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 14, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 13, 50, 50, 13, 13, 13, 13, 13, 6, 2, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 48, 49, 50]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468671012 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001468671012 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468671012/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468671012/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468671012 Building ZINC001468710043 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468710043' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468710043 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468710043 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468710043/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468710043 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 736) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/736 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/736' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@H](N2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2)C1) `ZINC001468710043.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468710043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468710043/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001468710043 none CC(C)(C)OC(=O)N1CC[C@H](N2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)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', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 30, 18, 10, 18, 10, 10, 10, 7, 10, 7, 7, 7, 4, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 10, 30, 30, 30, 30, 30, 30, 30, 30, 30, 10, 10, 10, 10, 7, 7, 7, 7, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 10, 10] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468710043 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468710043/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468710043 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 737) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/737 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/737' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@H](N2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2)C1) `ZINC001468710043.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468710043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468710043/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001468710043 none CC(C)(C)OC(=O)N1CC[C@H](N2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)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', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 12, 21, 12, 12, 12, 9, 12, 9, 9, 9, 5, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 12, 30, 30, 30, 30, 30, 30, 30, 30, 30, 12, 12, 12, 12, 9, 9, 9, 9, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 12, 12] 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: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468710043 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001468710043 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468710043/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468710043/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468710043 Building ZINC001468710043 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468710043' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468710043 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468710043 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468710043/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468710043 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 736) grep: /scratch/xiaobo/418326/xbt-8058088.46/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)N1CC[C@H](N2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2)C1) `ZINC001468710043.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468710043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468710043/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001468710043 none CC(C)(C)OC(=O)N1CC[C@H](N2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)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', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 30, 18, 10, 18, 10, 10, 10, 7, 10, 7, 7, 7, 4, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 10, 30, 30, 30, 30, 30, 30, 30, 30, 30, 10, 10, 10, 10, 7, 7, 7, 7, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 10, 10] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468710043 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468710043/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468710043 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 737) grep: /scratch/xiaobo/418326/xbt-8058088.46/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)N1CC[C@H](N2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2)C1) `ZINC001468710043.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468710043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468710043/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001468710043 none CC(C)(C)OC(=O)N1CC[C@H](N2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)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', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 12, 21, 12, 12, 12, 9, 12, 9, 9, 9, 5, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 12, 30, 30, 30, 30, 30, 30, 30, 30, 30, 12, 12, 12, 12, 9, 9, 9, 9, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 12, 12] 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: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468710043 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001468710043 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468710043/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468710043/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468710043 Building ZINC001468710046 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468710046' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468710046 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468710046 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468710046/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468710046 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 738) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/738 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/738' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@H](N2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2)C1) `ZINC001468710046.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468710046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468710046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001468710046 none CC(C)(C)OC(=O)N1CC[C@@H](N2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)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', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 30, 20, 12, 20, 12, 12, 12, 10, 12, 10, 10, 10, 4, 1, 2, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 10, 10, 12, 30, 30, 30, 30, 30, 30, 30, 30, 30, 12, 12, 12, 12, 10, 10, 10, 10, 6, 7, 7, 6, 7, 7, 6, 10, 10, 10, 10, 12, 12] 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: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468710046 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468710046/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468710046 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 739) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/739 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/739' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@H](N2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2)C1) `ZINC001468710046.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468710046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468710046/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001468710046 none CC(C)(C)OC(=O)N1CC[C@@H](N2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)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', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 13, 20, 13, 13, 13, 10, 13, 10, 10, 10, 5, 1, 3, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 10, 10, 13, 32, 32, 32, 32, 32, 32, 32, 32, 32, 13, 13, 13, 13, 10, 10, 10, 10, 6, 7, 7, 6, 7, 7, 6, 10, 10, 10, 10, 13, 13] 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: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468710046 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001468710046 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468710046/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468710046/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468710046 Building ZINC001468710046 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468710046' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468710046 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468710046 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468710046/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468710046 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 738) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/738: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@H](N2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2)C1) `ZINC001468710046.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468710046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468710046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001468710046 none CC(C)(C)OC(=O)N1CC[C@@H](N2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)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', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 30, 20, 12, 20, 12, 12, 12, 10, 12, 10, 10, 10, 4, 1, 2, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 10, 10, 12, 30, 30, 30, 30, 30, 30, 30, 30, 30, 12, 12, 12, 12, 10, 10, 10, 10, 6, 7, 7, 6, 7, 7, 6, 10, 10, 10, 10, 12, 12] 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: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468710046 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468710046/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468710046 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 739) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/739: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@H](N2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2)C1) `ZINC001468710046.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468710046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468710046/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001468710046 none CC(C)(C)OC(=O)N1CC[C@@H](N2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)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', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 13, 20, 13, 13, 13, 10, 13, 10, 10, 10, 5, 1, 3, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 10, 10, 13, 32, 32, 32, 32, 32, 32, 32, 32, 32, 13, 13, 13, 13, 10, 10, 10, 10, 6, 7, 7, 6, 7, 7, 6, 10, 10, 10, 10, 13, 13] 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: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468710046 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001468710046 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468710046/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468710046/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001468710046 Building ZINC001469283004 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001469283004' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001469283004 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469283004 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001469283004/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001469283004 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 740) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/740 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/740' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)C[C@H]2NC(=O)OC(C)(C)C)cn1) `ZINC001469283004.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469283004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001469283004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001469283004 none Cn1cc([C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)C[C@H]2NC(=O)OC(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 8, 8, 8, 8, 2, 1, 5, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 16, 26, 26, 26, 26, 26, 26, 21, 21, 21, 21, 21, 21, 8, 8, 3, 3, 3, 3, 3, 3, 3, 8, 8, 16, 26, 26, 26, 26, 26, 26, 26, 26, 26, 21] 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: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001469283004 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001469283004/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001469283004 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 741) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/741 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/741' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)C[C@H]2NC(=O)OC(C)(C)C)cn1) `ZINC001469283004.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469283004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001469283004/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001469283004 none Cn1cc([C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)C[C@H]2NC(=O)OC(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 5, 5, 5, 5, 1, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 14, 19, 19, 19, 19, 19, 19, 11, 11, 11, 11, 11, 11, 5, 5, 4, 4, 4, 4, 4, 4, 4, 5, 5, 14, 19, 19, 19, 19, 19, 19, 19, 19, 19, 11] 50 rigid atoms, others: [8, 10, 11, 12, 7] set([0, 1, 2, 3, 4, 5, 6, 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: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001469283004 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001469283004 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001469283004/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001469283004/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001469283004 Building ZINC001469283004 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001469283004' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001469283004 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469283004 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001469283004/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001469283004 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 740) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc([C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)C[C@H]2NC(=O)OC(C)(C)C)cn1) `ZINC001469283004.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469283004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001469283004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001469283004 none Cn1cc([C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)C[C@H]2NC(=O)OC(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 8, 8, 8, 8, 2, 1, 5, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 16, 26, 26, 26, 26, 26, 26, 21, 21, 21, 21, 21, 21, 8, 8, 3, 3, 3, 3, 3, 3, 3, 8, 8, 16, 26, 26, 26, 26, 26, 26, 26, 26, 26, 21] 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: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001469283004 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001469283004/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001469283004 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 741) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc([C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)C[C@H]2NC(=O)OC(C)(C)C)cn1) `ZINC001469283004.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469283004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001469283004/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001469283004 none Cn1cc([C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)C[C@H]2NC(=O)OC(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 5, 5, 5, 5, 1, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 14, 19, 19, 19, 19, 19, 19, 11, 11, 11, 11, 11, 11, 5, 5, 4, 4, 4, 4, 4, 4, 4, 5, 5, 14, 19, 19, 19, 19, 19, 19, 19, 19, 19, 11] 50 rigid atoms, others: [8, 10, 11, 12, 7] set([0, 1, 2, 3, 4, 5, 6, 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: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001469283004 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001469283004 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001469283004/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001469283004/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001469283004 Building ZINC001470361103 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470361103' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470361103 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001470361103 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470361103/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470361103 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 742) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/742 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/742' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCC(c2n[nH]c(CNC(=O)OCc3ccccc3)n2)CC1) `ZINC001470361103.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001470361103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470361103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001470361103 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCC(c2n[nH]c(CNC(=O)OCc3ccccc3)n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 8, 6, 1, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total 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, 2, 2, 2, 14, 14, 14, 14, 14, 25, 26, 26, 26, 26, 50, 50, 50, 50, 50, 50, 14, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 25, 25, 26, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 34, 35, 36, 5, 38, 39, 8, 9, 10, 7, 2, 3, 4, 6, 37] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470361103 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470361103/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470361103 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 743) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/743 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/743' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCC(c2n[nH]c(CNC(=O)OCc3ccccc3)n2)CC1) `ZINC001470361103.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001470361103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470361103/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001470361103 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCC(c2n[nH]c(CNC(=O)OCc3ccccc3)n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 8, 6, 1, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total 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, 2, 3, 3, 3, 3, 3, 17, 17, 17, 17, 17, 30, 31, 31, 31, 31, 50, 50, 50, 50, 50, 50, 17, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 30, 30, 31, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 34, 35, 36, 5, 38, 39, 8, 7, 2, 3, 4, 6, 37] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470361103 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001470361103 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470361103/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470361103/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470361103 Building ZINC001470361103 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470361103' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470361103 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001470361103 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470361103/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470361103 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 742) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCC(c2n[nH]c(CNC(=O)OCc3ccccc3)n2)CC1) `ZINC001470361103.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001470361103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470361103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001470361103 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCC(c2n[nH]c(CNC(=O)OCc3ccccc3)n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 8, 6, 1, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total 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, 2, 2, 2, 14, 14, 14, 14, 14, 25, 26, 26, 26, 26, 50, 50, 50, 50, 50, 50, 14, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 25, 25, 26, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 34, 35, 36, 5, 38, 39, 8, 9, 10, 7, 2, 3, 4, 6, 37] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470361103 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470361103/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470361103 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 743) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCC(c2n[nH]c(CNC(=O)OCc3ccccc3)n2)CC1) `ZINC001470361103.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001470361103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470361103/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001470361103 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCC(c2n[nH]c(CNC(=O)OCc3ccccc3)n2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 8, 6, 1, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total 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, 2, 3, 3, 3, 3, 3, 17, 17, 17, 17, 17, 30, 31, 31, 31, 31, 50, 50, 50, 50, 50, 50, 17, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 30, 30, 31, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 34, 35, 36, 5, 38, 39, 8, 7, 2, 3, 4, 6, 37] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470361103 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001470361103 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470361103/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470361103/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470361103 Building ZINC001470678271 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470678271' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470678271 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001470678271 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470678271/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470678271 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 744) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/744 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/744' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCc1cn(c2cccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(O)cc3)c2)nn1) `ZINC001470678271.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001470678271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470678271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001470678271 none CC(C)(C)OC(=O)NCc1cn(c2cccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(O)cc3)c2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 44, 50, 37, 11, 11, 11, 11, 11, 11, 11, 11, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 44, 37, 37, 11, 11, 11, 11, 8, 8, 2, 2, 2, 4, 2, 2, 11] 100 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]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470678271 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470678271/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470678271 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 745) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/745 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/745' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCc1cn(c2cccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(O)cc3)c2)nn1) `ZINC001470678271.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001470678271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470678271/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001470678271 none CC(C)(C)OC(=O)NCc1cn(c2cccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(O)cc3)c2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 49, 41, 49, 36, 10, 10, 10, 10, 10, 10, 10, 10, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 36, 36, 10, 10, 10, 10, 8, 8, 2, 2, 2, 4, 2, 2, 10] 100 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]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470678271 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001470678271 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470678271/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470678271/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470678271 Building ZINC001470678271 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470678271' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470678271 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001470678271 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470678271/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470678271 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 744) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/744: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCc1cn(c2cccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(O)cc3)c2)nn1) `ZINC001470678271.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001470678271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470678271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001470678271 none CC(C)(C)OC(=O)NCc1cn(c2cccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(O)cc3)c2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 44, 50, 37, 11, 11, 11, 11, 11, 11, 11, 11, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 44, 37, 37, 11, 11, 11, 11, 8, 8, 2, 2, 2, 4, 2, 2, 11] 100 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]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470678271 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470678271/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470678271 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 745) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/745: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCc1cn(c2cccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(O)cc3)c2)nn1) `ZINC001470678271.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001470678271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470678271/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001470678271 none CC(C)(C)OC(=O)NCc1cn(c2cccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(O)cc3)c2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 49, 41, 49, 36, 10, 10, 10, 10, 10, 10, 10, 10, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 36, 36, 10, 10, 10, 10, 8, 8, 2, 2, 2, 4, 2, 2, 10] 100 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]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470678271 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001470678271 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470678271/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470678271/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470678271 Building ZINC001470934529 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470934529' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470934529 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001470934529 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470934529/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470934529 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 746) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/746 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/746' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(c2ncc(I)cn2)CC1) `ZINC001470934529.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001470934529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470934529/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001470934529 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(c2ncc(I)cn2)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.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 8, 1, 1, 18, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 12, 22, 36, 36, 36, 36, 45, 45, 45, 45, 45, 45, 36, 36, 5, 5, 5, 5, 5, 5, 36, 36, 36, 36, 45, 45, 36, 36, 36, 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470934529 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470934529/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470934529 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 747) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/747 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/747' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN(c2ncc(I)cn2)CC1) `ZINC001470934529.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001470934529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470934529/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001470934529 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN(c2ncc(I)cn2)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.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 8, 1, 1, 18, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 11, 21, 34, 34, 34, 34, 46, 46, 34, 44, 46, 46, 34, 34, 5, 5, 5, 5, 5, 5, 34, 34, 34, 34, 46, 46, 34, 34, 34, 34] 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]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470934529 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001470934529 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470934529/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470934529/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470934529 Building ZINC001470934529 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470934529' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470934529 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001470934529 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470934529/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470934529 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 746) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(c2ncc(I)cn2)CC1) `ZINC001470934529.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001470934529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470934529/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001470934529 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(c2ncc(I)cn2)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.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 8, 1, 1, 18, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 12, 22, 36, 36, 36, 36, 45, 45, 45, 45, 45, 45, 36, 36, 5, 5, 5, 5, 5, 5, 36, 36, 36, 36, 45, 45, 36, 36, 36, 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470934529 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470934529/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470934529 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 747) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN(c2ncc(I)cn2)CC1) `ZINC001470934529.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001470934529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470934529/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001470934529 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN(c2ncc(I)cn2)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.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 8, 1, 1, 18, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 11, 21, 34, 34, 34, 34, 46, 46, 34, 44, 46, 46, 34, 34, 5, 5, 5, 5, 5, 5, 34, 34, 34, 34, 46, 46, 34, 34, 34, 34] 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]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470934529 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001470934529 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470934529/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470934529/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001470934529 Building ZINC001471658454 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001471658454' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001471658454 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471658454 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001471658454/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001471658454 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 748) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/748 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/748' -> `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)CC1(O)CN(C(=O)OC(C)(C)C)C1) `ZINC001471658454.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471658454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001471658454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001471658454 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(Cc1ccccc1)CC1(O)CN(C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 12, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 5, 5, 4, 5, 5, 2, 4, 6, 6, 6, 6, 15, 15, 37, 37, 37, 37, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 5, 5, 5, 5, 5, 4, 4, 18, 6, 6, 37, 37, 37, 37, 37, 37, 37, 37, 37, 6, 6] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 119 number of broken/clashed sets: 83 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001471658454 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001471658454/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001471658454 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 749) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/749 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/749' -> `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)CC1(O)CN(C(=O)OC(C)(C)C)C1) `ZINC001471658454.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471658454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001471658454/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001471658454 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(Cc1ccccc1)CC1(O)CN(C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 12, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 4, 7, 8, 8, 8, 8, 8, 4, 5, 6, 6, 6, 6, 15, 15, 34, 34, 34, 34, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 8, 8, 8, 8, 8, 5, 5, 18, 6, 6, 34, 34, 34, 34, 34, 34, 34, 34, 34, 6, 6] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 110 number of broken/clashed sets: 74 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001471658454 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001471658454 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001471658454/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001471658454/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001471658454 Building ZINC001471658454 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001471658454' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001471658454 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471658454 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001471658454/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001471658454 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 748) grep: /scratch/xiaobo/418326/xbt-8058088.46/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(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(Cc1ccccc1)CC1(O)CN(C(=O)OC(C)(C)C)C1) `ZINC001471658454.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471658454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001471658454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001471658454 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(Cc1ccccc1)CC1(O)CN(C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 12, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 5, 5, 4, 5, 5, 2, 4, 6, 6, 6, 6, 15, 15, 37, 37, 37, 37, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 5, 5, 5, 5, 5, 4, 4, 18, 6, 6, 37, 37, 37, 37, 37, 37, 37, 37, 37, 6, 6] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 119 number of broken/clashed sets: 83 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001471658454 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001471658454/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001471658454 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 749) grep: /scratch/xiaobo/418326/xbt-8058088.46/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(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(Cc1ccccc1)CC1(O)CN(C(=O)OC(C)(C)C)C1) `ZINC001471658454.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471658454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001471658454/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001471658454 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(Cc1ccccc1)CC1(O)CN(C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 12, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 4, 7, 8, 8, 8, 8, 8, 4, 5, 6, 6, 6, 6, 15, 15, 34, 34, 34, 34, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 8, 8, 8, 8, 8, 5, 5, 18, 6, 6, 34, 34, 34, 34, 34, 34, 34, 34, 34, 6, 6] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 110 number of broken/clashed sets: 74 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001471658454 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001471658454 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001471658454/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001471658454/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001471658454 Building ZINC001472567518 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001472567518' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001472567518 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472567518 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001472567518/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001472567518 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 750) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/750 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/750' -> `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(CN2CCOCC2)C1) `ZINC001472567518.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472567518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001472567518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472567518 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(CN2CCOCC2)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', 'N.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', '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, 10, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 6, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 1, 2, 3, 3, 3, 9, 11, 11, 11, 11, 11, 3, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 3, 3, 3, 9, 9, 11, 11, 11, 11, 11, 11, 11, 11, 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: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001472567518 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001472567518/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001472567518 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 751) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/751 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/751' -> `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(CN2CCOCC2)C1) `ZINC001472567518.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472567518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001472567518/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472567518 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(CN2CCOCC2)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', 'N.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', '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, 10, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 1, 2, 3, 3, 3, 9, 9, 9, 9, 9, 9, 3, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 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: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001472567518 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001472567518 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001472567518/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001472567518/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001472567518 Building ZINC001472567518 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001472567518' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001472567518 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472567518 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001472567518/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001472567518 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 750) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/750: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(CN2CCOCC2)C1) `ZINC001472567518.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472567518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001472567518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472567518 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(CN2CCOCC2)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', 'N.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', '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, 10, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 6, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 1, 2, 3, 3, 3, 9, 11, 11, 11, 11, 11, 3, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 3, 3, 3, 9, 9, 11, 11, 11, 11, 11, 11, 11, 11, 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: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001472567518 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001472567518/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001472567518 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 751) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/751: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(CN2CCOCC2)C1) `ZINC001472567518.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472567518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001472567518/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472567518 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(CN2CCOCC2)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', 'N.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', '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, 10, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 1, 2, 3, 3, 3, 9, 9, 9, 9, 9, 9, 3, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 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: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001472567518 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001472567518 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001472567518/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001472567518/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001472567518 Building ZINC001538460412 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001538460412' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001538460412 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001538460412 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001538460412/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001538460412 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 752) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/752 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/752' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCS(=O)(=O)c1ccc(CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1) `ZINC001538460412.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001538460412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001538460412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001538460412 none COCCS(=O)(=O)c1ccc(CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 14, 11, 11, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 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, 3, 7, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens 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, 39, 39, 21, 21, 21, 21, 8, 21, 21, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 21, 21, 45, 45, 45, 39, 39, 39, 39, 21, 21, 7, 7, 1, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 21, 21] 50 rigid atoms, others: [11, 43, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001538460412 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001538460412/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001538460412 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 753) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/753 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/753' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCS(=O)(=O)c1ccc(CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1) `ZINC001538460412.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001538460412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001538460412/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001538460412 none COCCS(=O)(=O)c1ccc(CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 14, 11, 11, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 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, 3, 7, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens 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, 39, 39, 21, 7, 21, 21, 7, 21, 21, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 21, 21, 45, 45, 45, 39, 39, 39, 39, 21, 21, 7, 7, 1, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 2, 21, 21] 50 rigid atoms, others: [11, 43, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 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/418326/xbt-8058088.46/working/building/ZINC001538460412 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001538460412 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001538460412/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001538460412/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001538460412 Building ZINC001538460412 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001538460412' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001538460412 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001538460412 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001538460412/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001538460412 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 752) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COCCS(=O)(=O)c1ccc(CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1) `ZINC001538460412.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001538460412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001538460412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001538460412 none COCCS(=O)(=O)c1ccc(CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 14, 11, 11, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 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, 3, 7, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens 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, 39, 39, 21, 21, 21, 21, 8, 21, 21, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 21, 21, 45, 45, 45, 39, 39, 39, 39, 21, 21, 7, 7, 1, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 21, 21] 50 rigid atoms, others: [11, 43, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001538460412 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001538460412/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001538460412 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 753) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COCCS(=O)(=O)c1ccc(CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1) `ZINC001538460412.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001538460412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001538460412/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001538460412 none COCCS(=O)(=O)c1ccc(CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 14, 11, 11, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 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, 3, 7, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens 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, 39, 39, 21, 7, 21, 21, 7, 21, 21, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 21, 21, 45, 45, 45, 39, 39, 39, 39, 21, 21, 7, 7, 1, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 2, 21, 21] 50 rigid atoms, others: [11, 43, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 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/418326/xbt-8058088.46/working/building/ZINC001538460412 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001538460412 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001538460412/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001538460412/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001538460412 Building ZINC001539048556 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001539048556' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001539048556 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001539048556 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001539048556/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001539048556 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 754) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/754 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/754' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(N3CCS(=O)(=O)CC3)cc2OC)cc1Cl) `ZINC001539048556.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001539048556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001539048556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001539048556 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(N3CCS(=O)(=O)CC3)cc2OC)cc1Cl NO_LONG_NAME dock atom 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.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 14, 11, 11, 5, 5, 1, 1, 12, 5, 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, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 6, 21, 21, 21, 21, 21, 21, 21, 4, 4, 4, 5, 4, 4, 4, 9, 9, 9, 4, 4, 2, 4, 4, 21, 21, 21, 21, 21, 21, 21, 21, 4, 5, 5, 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001539048556 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001539048556/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001539048556 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 755) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/755 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/755' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(N3CCS(=O)(=O)CC3)cc2OC)cc1Cl) `ZINC001539048556.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001539048556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001539048556/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001539048556 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(N3CCS(=O)(=O)CC3)cc2OC)cc1Cl NO_LONG_NAME dock atom 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.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 14, 11, 11, 5, 5, 1, 1, 12, 5, 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, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 5, 19, 19, 19, 19, 19, 19, 19, 4, 4, 4, 6, 4, 4, 4, 9, 9, 9, 4, 4, 2, 4, 4, 19, 19, 19, 19, 19, 19, 19, 19, 4, 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, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001539048556 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001539048556 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001539048556/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001539048556/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001539048556 Building ZINC001539048556 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001539048556' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001539048556 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001539048556 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001539048556/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001539048556 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 754) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(N3CCS(=O)(=O)CC3)cc2OC)cc1Cl) `ZINC001539048556.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001539048556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001539048556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001539048556 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(N3CCS(=O)(=O)CC3)cc2OC)cc1Cl NO_LONG_NAME dock atom 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.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 14, 11, 11, 5, 5, 1, 1, 12, 5, 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, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 6, 21, 21, 21, 21, 21, 21, 21, 4, 4, 4, 5, 4, 4, 4, 9, 9, 9, 4, 4, 2, 4, 4, 21, 21, 21, 21, 21, 21, 21, 21, 4, 5, 5, 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001539048556 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001539048556/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001539048556 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 755) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(N3CCS(=O)(=O)CC3)cc2OC)cc1Cl) `ZINC001539048556.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001539048556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001539048556/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001539048556 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(N3CCS(=O)(=O)CC3)cc2OC)cc1Cl NO_LONG_NAME dock atom 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.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 14, 11, 11, 5, 5, 1, 1, 12, 5, 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, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 5, 19, 19, 19, 19, 19, 19, 19, 4, 4, 4, 6, 4, 4, 4, 9, 9, 9, 4, 4, 2, 4, 4, 19, 19, 19, 19, 19, 19, 19, 19, 4, 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, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001539048556 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001539048556 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001539048556/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001539048556/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001539048556 Building ZINC001540028020 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540028020' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540028020 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001540028020 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540028020/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540028020 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 756) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/756 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/756' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCC(=O)Nc2ccc(I)cc2)cn1) `ZINC001540028020.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001540028020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540028020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001540028020 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCC(=O)Nc2ccc(I)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.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 1, 1, 1, 1, 18, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 12, 6, 6, 1, 1, 1, 1, 3, 3, 3, 9, 16, 16, 16, 28, 28, 16, 16, 28, 28, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 3, 9, 9, 16, 28, 28, 28, 28, 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]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540028020 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540028020/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540028020 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 757) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/757 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/757' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCC(=O)Nc2ccc(I)cc2)cn1) `ZINC001540028020.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001540028020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540028020/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001540028020 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCC(=O)Nc2ccc(I)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.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 1, 1, 1, 1, 18, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 14, 14, 6, 6, 1, 1, 1, 1, 4, 4, 4, 9, 17, 17, 17, 24, 24, 17, 17, 24, 24, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 4, 9, 9, 17, 24, 24, 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]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540028020 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001540028020 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540028020/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540028020/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540028020 Building ZINC001540028020 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540028020' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540028020 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001540028020 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540028020/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540028020 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 756) grep: /scratch/xiaobo/418326/xbt-8058088.46/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)n1cc([C@@]([O-])([SiH3])C(=O)NCC(=O)Nc2ccc(I)cc2)cn1) `ZINC001540028020.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001540028020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540028020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001540028020 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCC(=O)Nc2ccc(I)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.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 1, 1, 1, 1, 18, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 12, 6, 6, 1, 1, 1, 1, 3, 3, 3, 9, 16, 16, 16, 28, 28, 16, 16, 28, 28, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 3, 9, 9, 16, 28, 28, 28, 28, 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]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540028020 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540028020/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540028020 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 757) grep: /scratch/xiaobo/418326/xbt-8058088.46/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)n1cc([C@]([O-])([SiH3])C(=O)NCC(=O)Nc2ccc(I)cc2)cn1) `ZINC001540028020.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001540028020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540028020/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001540028020 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCC(=O)Nc2ccc(I)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.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 1, 1, 1, 1, 18, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 14, 14, 6, 6, 1, 1, 1, 1, 4, 4, 4, 9, 17, 17, 17, 24, 24, 17, 17, 24, 24, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 4, 9, 9, 17, 24, 24, 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]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540028020 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001540028020 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540028020/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540028020/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540028020 Building ZINC001540266700 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540266700' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540266700 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001540266700 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540266700/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540266700 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 758) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/758 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/758' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3cccc(Br)c3)CC2)c1) `ZINC001540266700.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001540266700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540266700/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001540266700 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3cccc(Br)c3)CC2)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', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 17, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 4, 6, 12, 12, 12, 12, 15, 15, 15, 28, 28, 26, 28, 28, 28, 12, 12, 2, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 28, 28, 26, 28, 12, 12, 12, 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]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540266700 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540266700/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540266700 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 759) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/759 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/759' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3cccc(Br)c3)CC2)c1) `ZINC001540266700.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001540266700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540266700/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001540266700 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3cccc(Br)c3)CC2)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', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 17, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 4, 4, 9, 9, 9, 9, 14, 14, 14, 26, 26, 26, 26, 26, 26, 9, 9, 4, 4, 4, 4, 2, 4, 4, 9, 9, 9, 9, 26, 26, 26, 26, 9, 9, 9, 9, 4] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540266700 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001540266700 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540266700/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540266700/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540266700 Building ZINC001540266700 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540266700' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540266700 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001540266700 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540266700/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540266700 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 758) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3cccc(Br)c3)CC2)c1) `ZINC001540266700.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001540266700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540266700/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001540266700 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3cccc(Br)c3)CC2)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', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 17, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 4, 6, 12, 12, 12, 12, 15, 15, 15, 28, 28, 26, 28, 28, 28, 12, 12, 2, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 28, 28, 26, 28, 12, 12, 12, 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]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540266700 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540266700/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540266700 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 759) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3cccc(Br)c3)CC2)c1) `ZINC001540266700.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001540266700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540266700/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001540266700 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN(S(=O)(=O)c3cccc(Br)c3)CC2)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', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 17, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 4, 4, 9, 9, 9, 9, 14, 14, 14, 26, 26, 26, 26, 26, 26, 9, 9, 4, 4, 4, 4, 2, 4, 4, 9, 9, 9, 9, 26, 26, 26, 26, 9, 9, 9, 9, 4] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540266700 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001540266700 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540266700/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540266700/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540266700 Building ZINC001540289897 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540289897' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540289897 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001540289897 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540289897/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540289897 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 760) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/760 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/760' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(NS(=O)(=O)c2ccc(OC)c(NC(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)c2)cc1) `ZINC001540289897.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001540289897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540289897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001540289897 none CCOc1ccc(NS(=O)(=O)c2ccc(OC)c(NC(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', '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, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 25, 30, 30, 18, 10, 6, 10, 10, 6, 4, 6, 6, 6, 10, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 30, 30, 37, 37, 37, 37, 37, 30, 30, 18, 6, 6, 10, 10, 10, 2, 6, 6, 6, 6, 6, 6, 30, 30] 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]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540289897 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540289897/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540289897 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 761) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/761 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/761' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(NS(=O)(=O)c2ccc(OC)c(NC(=O)[C@]([O-])([SiH3])c3cnn(C)c3)c2)cc1) `ZINC001540289897.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001540289897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540289897/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001540289897 none CCOc1ccc(NS(=O)(=O)c2ccc(OC)c(NC(=O)[C@]([O-])([SiH3])c3cnn(C)c3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', '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, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 39, 29, 18, 32, 32, 18, 10, 6, 10, 10, 6, 6, 6, 6, 6, 10, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 32, 32, 40, 40, 40, 40, 40, 32, 32, 18, 6, 6, 10, 10, 10, 2, 6, 6, 6, 6, 6, 6, 32, 32] 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]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540289897 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001540289897 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540289897/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540289897/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540289897 Building ZINC001540289897 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540289897' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540289897 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001540289897 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540289897/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540289897 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 760) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCOc1ccc(NS(=O)(=O)c2ccc(OC)c(NC(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)c2)cc1) `ZINC001540289897.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001540289897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540289897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001540289897 none CCOc1ccc(NS(=O)(=O)c2ccc(OC)c(NC(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', '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, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 25, 30, 30, 18, 10, 6, 10, 10, 6, 4, 6, 6, 6, 10, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 30, 30, 37, 37, 37, 37, 37, 30, 30, 18, 6, 6, 10, 10, 10, 2, 6, 6, 6, 6, 6, 6, 30, 30] 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]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540289897 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540289897/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540289897 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 761) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCOc1ccc(NS(=O)(=O)c2ccc(OC)c(NC(=O)[C@]([O-])([SiH3])c3cnn(C)c3)c2)cc1) `ZINC001540289897.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001540289897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540289897/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001540289897 none CCOc1ccc(NS(=O)(=O)c2ccc(OC)c(NC(=O)[C@]([O-])([SiH3])c3cnn(C)c3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', '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, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 39, 29, 18, 32, 32, 18, 10, 6, 10, 10, 6, 6, 6, 6, 6, 10, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 32, 32, 40, 40, 40, 40, 40, 32, 32, 18, 6, 6, 10, 10, 10, 2, 6, 6, 6, 6, 6, 6, 32, 32] 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]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540289897 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001540289897 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540289897/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540289897/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540289897 Building ZINC001540429345 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540429345' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540429345 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001540429345 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540429345/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540429345 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 762) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/762 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/762' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(S(=O)(=O)c2ccc(F)cc2F)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001540429345.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001540429345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540429345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001540429345 none O=C(N1CCN(S(=O)(=O)c2ccc(F)cc2F)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 15, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 14, 14, 14, 14, 20, 20, 20, 40, 40, 35, 40, 40, 40, 40, 14, 14, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 40, 40, 40, 14, 14, 14, 14, 3, 3, 3, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540429345 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540429345/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540429345 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 763) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/763 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/763' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(S(=O)(=O)c2ccc(F)cc2F)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001540429345.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001540429345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540429345/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001540429345 none O=C(N1CCN(S(=O)(=O)c2ccc(F)cc2F)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 15, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 10, 10, 10, 18, 18, 18, 35, 35, 32, 34, 35, 35, 35, 10, 10, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 35, 35, 35, 10, 10, 10, 10, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540429345 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001540429345 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540429345/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540429345/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540429345 Building ZINC001540429345 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540429345' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540429345 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001540429345 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540429345/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540429345 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 762) grep: /scratch/xiaobo/418326/xbt-8058088.46/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(N1CCN(S(=O)(=O)c2ccc(F)cc2F)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001540429345.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001540429345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540429345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001540429345 none O=C(N1CCN(S(=O)(=O)c2ccc(F)cc2F)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 15, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 14, 14, 14, 14, 20, 20, 20, 40, 40, 35, 40, 40, 40, 40, 14, 14, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 40, 40, 40, 14, 14, 14, 14, 3, 3, 3, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540429345 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540429345/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540429345 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 763) grep: /scratch/xiaobo/418326/xbt-8058088.46/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(N1CCN(S(=O)(=O)c2ccc(F)cc2F)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001540429345.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001540429345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540429345/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001540429345 none O=C(N1CCN(S(=O)(=O)c2ccc(F)cc2F)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 15, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 10, 10, 10, 18, 18, 18, 35, 35, 32, 34, 35, 35, 35, 10, 10, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 35, 35, 35, 10, 10, 10, 10, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540429345 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001540429345 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540429345/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540429345/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540429345 Building ZINC001540457356 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457356' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457356 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001540457356 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457356/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457356 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 764) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/764 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/764' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@H](C)CN(C(=O)CN2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)C1) `ZINC001540457356.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001540457356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001540457356 none C[C@H]1C[C@H](C)CN(C(=O)CN2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 40, 40, 40, 40, 34, 20, 34, 8, 8, 8, 8, 4, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 8, 8, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 15, 15, 8, 8, 8, 8, 3, 3, 8, 8, 8, 8, 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]) total number of confs: 113 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457356 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457356/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457356 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 765) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/765 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/765' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@H](C)CN(C(=O)CN2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)C1) `ZINC001540457356.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001540457356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457356/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001540457356 none C[C@H]1C[C@H](C)CN(C(=O)CN2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 42, 42, 42, 42, 39, 29, 39, 9, 9, 9, 9, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 21, 21, 9, 9, 9, 9, 2, 2, 9, 9, 9, 9, 42, 42] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 126 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457356 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001540457356 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457356/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457356/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457356 Building ZINC001540457356 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457356' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457356 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001540457356 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457356/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457356 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 764) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: C[C@H]1C[C@H](C)CN(C(=O)CN2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)C1) `ZINC001540457356.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001540457356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001540457356 none C[C@H]1C[C@H](C)CN(C(=O)CN2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 40, 40, 40, 40, 34, 20, 34, 8, 8, 8, 8, 4, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 8, 8, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 15, 15, 8, 8, 8, 8, 3, 3, 8, 8, 8, 8, 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]) total number of confs: 113 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457356 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457356/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457356 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 765) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: C[C@H]1C[C@H](C)CN(C(=O)CN2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)C1) `ZINC001540457356.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001540457356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457356/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001540457356 none C[C@H]1C[C@H](C)CN(C(=O)CN2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 42, 42, 42, 42, 39, 29, 39, 9, 9, 9, 9, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 21, 21, 9, 9, 9, 9, 2, 2, 9, 9, 9, 9, 42, 42] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 126 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457356 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001540457356 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457356/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457356/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457356 Building ZINC001540457357 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457357' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457357 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001540457357 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457357/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457357 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 766) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/766 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/766' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H](C)CN(C(=O)CN2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)C1) `ZINC001540457357.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001540457357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001540457357 none C[C@@H]1C[C@H](C)CN(C(=O)CN2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 42, 42, 42, 42, 42, 25, 42, 7, 7, 7, 7, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 7, 7, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 22, 22, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 42, 42] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 142 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457357 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457357/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457357 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 767) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/767 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/767' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H](C)CN(C(=O)CN2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)C1) `ZINC001540457357.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001540457357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457357/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001540457357 none C[C@@H]1C[C@H](C)CN(C(=O)CN2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 40, 40, 40, 40, 39, 25, 39, 7, 7, 7, 7, 4, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 7, 7, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 18, 18, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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]) total number of confs: 119 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457357 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001540457357 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457357/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457357/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457357 Building ZINC001540457357 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457357' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457357 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001540457357 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457357/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457357 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 766) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/766: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H](C)CN(C(=O)CN2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)C1) `ZINC001540457357.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001540457357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001540457357 none C[C@@H]1C[C@H](C)CN(C(=O)CN2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 42, 42, 42, 42, 42, 25, 42, 7, 7, 7, 7, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 7, 7, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 22, 22, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 42, 42] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 142 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457357 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457357/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457357 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 767) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/767: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H](C)CN(C(=O)CN2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)C1) `ZINC001540457357.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001540457357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457357/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001540457357 none C[C@@H]1C[C@H](C)CN(C(=O)CN2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 40, 40, 40, 40, 39, 25, 39, 7, 7, 7, 7, 4, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 7, 7, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 18, 18, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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]) total number of confs: 119 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457357 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001540457357 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457357/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457357/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457357 Building ZINC001540457358 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457358' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457358 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001540457358 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457358/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457358 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 768) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/768 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/768' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H](C)CN(C(=O)CN2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)C1) `ZINC001540457358.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001540457358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001540457358 none C[C@@H]1C[C@@H](C)CN(C(=O)CN2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 42, 42, 42, 42, 38, 26, 38, 9, 9, 9, 9, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 21, 21, 9, 9, 9, 9, 2, 2, 9, 9, 9, 9, 42, 42] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 129 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457358 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457358/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457358 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 769) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/769 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/769' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H](C)CN(C(=O)CN2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)C1) `ZINC001540457358.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001540457358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457358/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001540457358 none C[C@@H]1C[C@@H](C)CN(C(=O)CN2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 40, 40, 40, 40, 35, 24, 35, 8, 8, 8, 8, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 17, 17, 8, 8, 8, 8, 4, 4, 8, 8, 8, 8, 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]) total number of confs: 116 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457358 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001540457358 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457358/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457358/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457358 Building ZINC001540457358 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457358' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457358 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001540457358 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457358/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457358 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 768) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/768: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H](C)CN(C(=O)CN2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)C1) `ZINC001540457358.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001540457358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001540457358 none C[C@@H]1C[C@@H](C)CN(C(=O)CN2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 42, 42, 42, 42, 38, 26, 38, 9, 9, 9, 9, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 21, 21, 9, 9, 9, 9, 2, 2, 9, 9, 9, 9, 42, 42] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 129 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457358 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457358/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457358 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 769) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/769: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H](C)CN(C(=O)CN2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)C1) `ZINC001540457358.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001540457358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457358/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001540457358 none C[C@@H]1C[C@@H](C)CN(C(=O)CN2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 5, 8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 40, 40, 40, 40, 35, 24, 35, 8, 8, 8, 8, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 17, 17, 8, 8, 8, 8, 4, 4, 8, 8, 8, 8, 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]) total number of confs: 116 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457358 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001540457358 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457358/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457358/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540457358 Building ZINC001540674107 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540674107' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540674107 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001540674107 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540674107/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540674107 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 770) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/770 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/770' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCN(S(=O)(=O)c2cccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)CC1) `ZINC001540674107.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001540674107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540674107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001540674107 none CCN1CCN(S(=O)(=O)c2cccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'F', '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'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 32, 32, 32, 31, 25, 10, 25, 25, 10, 3, 10, 10, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 32, 32, 32, 34, 34, 34, 34, 32, 32, 32, 32, 3, 10, 10, 3, 4, 4, 4, 4, 10, 32, 32, 32, 32] 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: 126 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540674107 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540674107/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540674107 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 771) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/771 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/771' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCN(S(=O)(=O)c2cccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)CC1) `ZINC001540674107.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001540674107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540674107/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001540674107 none CCN1CCN(S(=O)(=O)c2cccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'F', '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'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 33, 33, 32, 26, 10, 26, 26, 10, 4, 10, 10, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 33, 33, 33, 35, 35, 35, 35, 33, 33, 33, 33, 9, 10, 10, 3, 4, 4, 4, 4, 10, 33, 33, 33, 33] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 141 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540674107 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001540674107 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540674107/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540674107/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540674107 Building ZINC001540674107 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540674107' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540674107 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001540674107 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540674107/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540674107 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 770) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCN1CCN(S(=O)(=O)c2cccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)CC1) `ZINC001540674107.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001540674107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540674107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001540674107 none CCN1CCN(S(=O)(=O)c2cccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'F', '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'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 32, 32, 32, 31, 25, 10, 25, 25, 10, 3, 10, 10, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 32, 32, 32, 34, 34, 34, 34, 32, 32, 32, 32, 3, 10, 10, 3, 4, 4, 4, 4, 10, 32, 32, 32, 32] 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: 126 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540674107 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540674107/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540674107 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 771) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCN1CCN(S(=O)(=O)c2cccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)CC1) `ZINC001540674107.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001540674107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540674107/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001540674107 none CCN1CCN(S(=O)(=O)c2cccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'F', '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'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 33, 33, 32, 26, 10, 26, 26, 10, 4, 10, 10, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 33, 33, 33, 35, 35, 35, 35, 33, 33, 33, 33, 9, 10, 10, 3, 4, 4, 4, 4, 10, 33, 33, 33, 33] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 141 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540674107 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001540674107 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540674107/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540674107/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540674107 Building ZINC001540808312 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540808312' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540808312 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001540808312 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540808312/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540808312 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 772) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/772 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/772' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)Cc1ccc(C(=O)C2CCN(C(=O)[C@@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)CC2)cc1) `ZINC001540808312.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001540808312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540808312/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001540808312 none CC(C)Cc1ccc(C(=O)C2CCN(C(=O)[C@@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 13, 4, 13, 4, 4, 4, 2, 1, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 4, 4, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 4, 4, 4, 4, 4, 1, 3, 3, 1, 1, 1, 1, 4, 4, 4, 4, 35, 35] 50 rigid atoms, others: [48, 51, 14, 16, 17, 18, 19, 20, 21, 54, 25, 26, 27, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 55, 56, 57, 58, 59, 60]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540808312 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540808312/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540808312 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 773) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/773 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/773' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)Cc1ccc(C(=O)C2CCN(C(=O)[C@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)CC2)cc1) `ZINC001540808312.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001540808312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540808312/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001540808312 none CC(C)Cc1ccc(C(=O)C2CCN(C(=O)[C@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 26, 26, 12, 3, 12, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 3, 3, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 3, 3, 3, 3, 3, 1, 4, 4, 1, 1, 1, 1, 3, 3, 3, 3, 26, 26] 50 rigid atoms, others: [48, 51, 14, 16, 17, 18, 19, 20, 21, 54, 25, 26, 27, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 55, 56, 57, 58, 59, 60]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540808312 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001540808312 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540808312/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540808312/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540808312 Building ZINC001540808312 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540808312' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540808312 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001540808312 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540808312/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540808312 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 772) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC(C)Cc1ccc(C(=O)C2CCN(C(=O)[C@@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)CC2)cc1) `ZINC001540808312.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001540808312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540808312/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001540808312 none CC(C)Cc1ccc(C(=O)C2CCN(C(=O)[C@@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 13, 4, 13, 4, 4, 4, 2, 1, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 4, 4, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 4, 4, 4, 4, 4, 1, 3, 3, 1, 1, 1, 1, 4, 4, 4, 4, 35, 35] 50 rigid atoms, others: [48, 51, 14, 16, 17, 18, 19, 20, 21, 54, 25, 26, 27, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 55, 56, 57, 58, 59, 60]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540808312 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540808312/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540808312 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 773) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC(C)Cc1ccc(C(=O)C2CCN(C(=O)[C@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)CC2)cc1) `ZINC001540808312.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001540808312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540808312/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001540808312 none CC(C)Cc1ccc(C(=O)C2CCN(C(=O)[C@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 26, 26, 12, 3, 12, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 3, 3, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 3, 3, 3, 3, 3, 1, 4, 4, 1, 1, 1, 1, 3, 3, 3, 3, 26, 26] 50 rigid atoms, others: [48, 51, 14, 16, 17, 18, 19, 20, 21, 54, 25, 26, 27, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 55, 56, 57, 58, 59, 60]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540808312 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001540808312 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540808312/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540808312/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001540808312 Building ZINC001542743671 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542743671' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542743671 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001542743671 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542743671/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542743671 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 774) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/774 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/774' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)N1CCN(Cc2ccccc2)CC1) `ZINC001542743671.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001542743671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542743671/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001542743671 none O=C(CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)N1CCN(Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.am', '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'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 10, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 17, 18, 18, 18, 18, 29, 39, 39, 39, 39, 39, 18, 18, 10, 10, 3, 7, 7, 18, 18, 18, 18, 29, 29, 39, 39, 39, 39, 39, 18, 18, 18, 18] 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]) total number of confs: 154 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542743671 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542743671/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542743671 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 775) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/775 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/775' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)N1CCN(Cc2ccccc2)CC1) `ZINC001542743671.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001542743671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542743671/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001542743671 none O=C(CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)N1CCN(Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.am', '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'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 16, 17, 17, 17, 17, 26, 38, 38, 38, 38, 38, 17, 17, 10, 10, 3, 7, 7, 17, 17, 17, 17, 26, 26, 38, 38, 38, 38, 38, 17, 17, 17, 17] 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]) total number of confs: 144 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542743671 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001542743671 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542743671/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542743671/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542743671 Building ZINC001542743671 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542743671' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542743671 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001542743671 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542743671/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542743671 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 774) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: O=C(CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)N1CCN(Cc2ccccc2)CC1) `ZINC001542743671.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001542743671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542743671/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001542743671 none O=C(CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)N1CCN(Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.am', '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'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 10, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 17, 18, 18, 18, 18, 29, 39, 39, 39, 39, 39, 18, 18, 10, 10, 3, 7, 7, 18, 18, 18, 18, 29, 29, 39, 39, 39, 39, 39, 18, 18, 18, 18] 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]) total number of confs: 154 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542743671 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542743671/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542743671 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 775) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: O=C(CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)N1CCN(Cc2ccccc2)CC1) `ZINC001542743671.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001542743671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542743671/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001542743671 none O=C(CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)N1CCN(Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.am', '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'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 16, 17, 17, 17, 17, 26, 38, 38, 38, 38, 38, 17, 17, 10, 10, 3, 7, 7, 17, 17, 17, 17, 26, 26, 38, 38, 38, 38, 38, 17, 17, 17, 17] 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]) total number of confs: 144 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542743671 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001542743671 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542743671/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542743671/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542743671 Building ZINC001542766799 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542766799' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542766799 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001542766799 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542766799/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542766799 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 776) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/776 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/776' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCn1c(=O)nc(O)c(NCc2ccccc2)c1NC(=O)[C@@]([O-])([SiH3])c1ccccc1OC) `ZINC001542766799.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001542766799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542766799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001542766799 none COCCn1c(=O)nc(O)c(NCc2ccccc2)c1NC(=O)[C@@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'O.3', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 8, 1, 12, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [23, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 24, 34, 36, 36, 34, 36, 36, 10, 8, 1, 8, 1, 1, 1, 7, 7, 2, 7, 7, 7, 7, 23, 23, 23, 22, 22, 22, 22, 66, 24, 34, 34, 36, 36, 34, 36, 36, 10, 7, 7, 7, 7, 7, 7, 7] 150 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 209 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542766799 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542766799/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542766799 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 777) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/777 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/777' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCn1c(=O)nc(O)c(NCc2ccccc2)c1NC(=O)[C@]([O-])([SiH3])c1ccccc1OC) `ZINC001542766799.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001542766799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542766799/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001542766799 none COCCn1c(=O)nc(O)c(NCc2ccccc2)c1NC(=O)[C@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'O.3', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 8, 1, 12, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [26, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 28, 38, 40, 40, 38, 40, 40, 13, 9, 1, 9, 1, 1, 1, 4, 4, 2, 4, 4, 4, 4, 26, 26, 26, 24, 24, 24, 24, 72, 28, 38, 38, 40, 40, 38, 40, 40, 13, 4, 4, 4, 4, 4, 4, 4] 150 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 216 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542766799 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001542766799 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542766799/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542766799/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542766799 Building ZINC001542766799 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542766799' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542766799 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001542766799 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542766799/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542766799 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 776) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COCCn1c(=O)nc(O)c(NCc2ccccc2)c1NC(=O)[C@@]([O-])([SiH3])c1ccccc1OC) `ZINC001542766799.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001542766799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542766799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001542766799 none COCCn1c(=O)nc(O)c(NCc2ccccc2)c1NC(=O)[C@@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'O.3', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 8, 1, 12, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [23, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 24, 34, 36, 36, 34, 36, 36, 10, 8, 1, 8, 1, 1, 1, 7, 7, 2, 7, 7, 7, 7, 23, 23, 23, 22, 22, 22, 22, 66, 24, 34, 34, 36, 36, 34, 36, 36, 10, 7, 7, 7, 7, 7, 7, 7] 150 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 209 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542766799 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542766799/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542766799 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 777) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COCCn1c(=O)nc(O)c(NCc2ccccc2)c1NC(=O)[C@]([O-])([SiH3])c1ccccc1OC) `ZINC001542766799.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001542766799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542766799/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001542766799 none COCCn1c(=O)nc(O)c(NCc2ccccc2)c1NC(=O)[C@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'O.3', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 8, 1, 12, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [26, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 28, 38, 40, 40, 38, 40, 40, 13, 9, 1, 9, 1, 1, 1, 4, 4, 2, 4, 4, 4, 4, 26, 26, 26, 24, 24, 24, 24, 72, 28, 38, 38, 40, 40, 38, 40, 40, 13, 4, 4, 4, 4, 4, 4, 4] 150 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 216 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542766799 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001542766799 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542766799/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542766799/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542766799 Building ZINC001542835071 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542835071' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542835071 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001542835071 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542835071/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542835071 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 778) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/778 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/778' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccnn1Cc1cccc(Cl)c1Cl) `ZINC001542835071.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001542835071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542835071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001542835071 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccnn1Cc1cccc(Cl)c1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', '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.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 1, 1, 2, 2, 5, 10, 10, 10, 10, 10, 24, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 4, 4, 1, 5, 10, 10, 24, 24, 26, 26, 26] 50 rigid atoms, others: [0, 1, 2, 3, 4, 32, 8, 9, 10, 11, 12, 35, 29, 30, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542835071 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542835071/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542835071 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 779) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/779 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/779' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ccnn1Cc1cccc(Cl)c1Cl) `ZINC001542835071.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001542835071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542835071/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001542835071 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ccnn1Cc1cccc(Cl)c1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', '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.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 1, 1, 2, 2, 5, 10, 10, 10, 10, 10, 24, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 4, 4, 1, 5, 10, 10, 24, 24, 26, 26, 26] 50 rigid atoms, others: [0, 1, 2, 3, 4, 32, 8, 9, 10, 11, 12, 35, 29, 30, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542835071 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001542835071 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542835071/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542835071/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542835071 Building ZINC001542835071 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542835071' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542835071 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001542835071 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542835071/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542835071 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 778) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/778: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccnn1Cc1cccc(Cl)c1Cl) `ZINC001542835071.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001542835071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542835071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001542835071 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccnn1Cc1cccc(Cl)c1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', '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.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 1, 1, 2, 2, 5, 10, 10, 10, 10, 10, 24, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 4, 4, 1, 5, 10, 10, 24, 24, 26, 26, 26] 50 rigid atoms, others: [0, 1, 2, 3, 4, 32, 8, 9, 10, 11, 12, 35, 29, 30, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542835071 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542835071/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542835071 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 779) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/779: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ccnn1Cc1cccc(Cl)c1Cl) `ZINC001542835071.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001542835071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542835071/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001542835071 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ccnn1Cc1cccc(Cl)c1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', '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.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 1, 1, 2, 2, 5, 10, 10, 10, 10, 10, 24, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 4, 4, 1, 5, 10, 10, 24, 24, 26, 26, 26] 50 rigid atoms, others: [0, 1, 2, 3, 4, 32, 8, 9, 10, 11, 12, 35, 29, 30, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542835071 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001542835071 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542835071/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542835071/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542835071 Building ZINC001542843221 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542843221' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542843221 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001542843221 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542843221/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542843221 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 780) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/780 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/780' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC1(c2ccc(Br)cc2)CCCC1) `ZINC001542843221.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001542843221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542843221/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001542843221 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC1(c2ccc(Br)cc2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 14, 4, 1, 1, 1, 1, 4, 4, 8, 12, 13, 13, 13, 13, 13, 13, 12, 12, 12, 12, 4, 4, 4, 4, 14, 14, 4, 4, 13, 13, 13, 13, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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/418326/xbt-8058088.46/working/building/ZINC001542843221 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542843221/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542843221 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 781) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/781 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/781' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC1(c2ccc(Br)cc2)CCCC1) `ZINC001542843221.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001542843221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542843221/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001542843221 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC1(c2ccc(Br)cc2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 14, 4, 1, 1, 1, 1, 4, 4, 7, 11, 13, 13, 11, 11, 13, 13, 11, 11, 11, 11, 4, 4, 4, 4, 14, 14, 4, 4, 13, 13, 13, 13, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542843221 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001542843221 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542843221/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542843221/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542843221 Building ZINC001542843221 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542843221' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542843221 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001542843221 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542843221/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542843221 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 780) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/780: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC1(c2ccc(Br)cc2)CCCC1) `ZINC001542843221.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001542843221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542843221/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001542843221 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC1(c2ccc(Br)cc2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 14, 4, 1, 1, 1, 1, 4, 4, 8, 12, 13, 13, 13, 13, 13, 13, 12, 12, 12, 12, 4, 4, 4, 4, 14, 14, 4, 4, 13, 13, 13, 13, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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/418326/xbt-8058088.46/working/building/ZINC001542843221 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542843221/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542843221 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 781) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/781: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC1(c2ccc(Br)cc2)CCCC1) `ZINC001542843221.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001542843221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542843221/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001542843221 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC1(c2ccc(Br)cc2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 14, 4, 1, 1, 1, 1, 4, 4, 7, 11, 13, 13, 11, 11, 13, 13, 11, 11, 11, 11, 4, 4, 4, 4, 14, 14, 4, 4, 13, 13, 13, 13, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542843221 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001542843221 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542843221/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542843221/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542843221 Building ZINC001542877497 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001542877497 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 782) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/782 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/782' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)C[N@]1CC[N@](C)CC1)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1) `ZINC001542877497.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001542877497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001542877497 none CN(C(=O)C[N@]1CC[N@](C)CC1)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 33, 34, 34, 34, 34, 34, 34, 6, 10, 10, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 16, 16, 16, 33, 33, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 10, 10, 3, 4, 4, 4, 4, 10, 10] 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]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 783) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/783 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/783' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)C[N@]1CC[N@@](C)CC1)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1) `ZINC001542877497.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001542877497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001542877497 none CN(C(=O)C[N@]1CC[N@@](C)CC1)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 10, 17, 22, 22, 33, 34, 34, 34, 34, 34, 34, 3, 10, 10, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 17, 17, 17, 33, 33, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 10, 10, 3, 4, 4, 4, 4, 10, 10] 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]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 784) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/784 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/784' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)C[N@]1CC[N@](C)CC1)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1) `ZINC001542877497.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001542877497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001542877497 none CN(C(=O)C[N@]1CC[N@](C)CC1)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 16, 21, 22, 33, 34, 34, 34, 34, 34, 34, 3, 10, 10, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 17, 17, 17, 33, 33, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 10, 10, 3, 4, 4, 4, 4, 10, 10] 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]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 785) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/785 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/785' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)C[N@]1CC[N@@](C)CC1)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1) `ZINC001542877497.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001542877497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001542877497 none CN(C(=O)C[N@]1CC[N@@](C)CC1)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 10, 18, 24, 24, 34, 35, 35, 35, 35, 35, 35, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 18, 18, 18, 34, 34, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 10, 10, 3, 4, 4, 4, 4, 10, 10] 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]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001542877497 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497 Building ZINC001542877497 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001542877497 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 782) grep: /scratch/xiaobo/418326/xbt-8058088.46/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(C(=O)C[N@]1CC[N@](C)CC1)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1) `ZINC001542877497.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001542877497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001542877497 none CN(C(=O)C[N@]1CC[N@](C)CC1)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 33, 34, 34, 34, 34, 34, 34, 6, 10, 10, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 16, 16, 16, 33, 33, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 10, 10, 3, 4, 4, 4, 4, 10, 10] 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]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 783) grep: /scratch/xiaobo/418326/xbt-8058088.46/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(C(=O)C[N@]1CC[N@@](C)CC1)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1) `ZINC001542877497.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001542877497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001542877497 none CN(C(=O)C[N@]1CC[N@@](C)CC1)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 10, 17, 22, 22, 33, 34, 34, 34, 34, 34, 34, 3, 10, 10, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 17, 17, 17, 33, 33, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 10, 10, 3, 4, 4, 4, 4, 10, 10] 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]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 784) grep: /scratch/xiaobo/418326/xbt-8058088.46/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(C(=O)C[N@]1CC[N@](C)CC1)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1) `ZINC001542877497.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001542877497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001542877497 none CN(C(=O)C[N@]1CC[N@](C)CC1)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 16, 21, 22, 33, 34, 34, 34, 34, 34, 34, 3, 10, 10, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 17, 17, 17, 33, 33, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 10, 10, 3, 4, 4, 4, 4, 10, 10] 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]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 785) grep: /scratch/xiaobo/418326/xbt-8058088.46/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(C(=O)C[N@]1CC[N@@](C)CC1)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1) `ZINC001542877497.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001542877497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001542877497 none CN(C(=O)C[N@]1CC[N@@](C)CC1)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 10, 18, 24, 24, 34, 35, 35, 35, 35, 35, 35, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 18, 18, 18, 34, 34, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 10, 10, 3, 4, 4, 4, 4, 10, 10] 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]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001542877497 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497 Building ZINC001542877497 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001542877497 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 782) grep: /scratch/xiaobo/418326/xbt-8058088.46/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(C(=O)C[N@]1CC[N@](C)CC1)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1) `ZINC001542877497.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001542877497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001542877497 none CN(C(=O)C[N@]1CC[N@](C)CC1)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 33, 34, 34, 34, 34, 34, 34, 6, 10, 10, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 16, 16, 16, 33, 33, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 10, 10, 3, 4, 4, 4, 4, 10, 10] 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]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 783) grep: /scratch/xiaobo/418326/xbt-8058088.46/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(C(=O)C[N@]1CC[N@@](C)CC1)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1) `ZINC001542877497.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001542877497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001542877497 none CN(C(=O)C[N@]1CC[N@@](C)CC1)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 10, 17, 22, 22, 33, 34, 34, 34, 34, 34, 34, 3, 10, 10, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 17, 17, 17, 33, 33, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 10, 10, 3, 4, 4, 4, 4, 10, 10] 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]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 784) grep: /scratch/xiaobo/418326/xbt-8058088.46/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(C(=O)C[N@]1CC[N@](C)CC1)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1) `ZINC001542877497.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001542877497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001542877497 none CN(C(=O)C[N@]1CC[N@](C)CC1)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 16, 21, 22, 33, 34, 34, 34, 34, 34, 34, 3, 10, 10, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 17, 17, 17, 33, 33, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 10, 10, 3, 4, 4, 4, 4, 10, 10] 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]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 785) grep: /scratch/xiaobo/418326/xbt-8058088.46/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(C(=O)C[N@]1CC[N@@](C)CC1)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1) `ZINC001542877497.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001542877497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001542877497 none CN(C(=O)C[N@]1CC[N@@](C)CC1)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 10, 18, 24, 24, 34, 35, 35, 35, 35, 35, 35, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 18, 18, 18, 34, 34, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 10, 10, 3, 4, 4, 4, 4, 10, 10] 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]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001542877497 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497 Building ZINC001542877497 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001542877497 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 782) grep: /scratch/xiaobo/418326/xbt-8058088.46/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(C(=O)C[N@]1CC[N@](C)CC1)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1) `ZINC001542877497.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001542877497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001542877497 none CN(C(=O)C[N@]1CC[N@](C)CC1)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 33, 34, 34, 34, 34, 34, 34, 6, 10, 10, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 16, 16, 16, 33, 33, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 10, 10, 3, 4, 4, 4, 4, 10, 10] 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]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 783) grep: /scratch/xiaobo/418326/xbt-8058088.46/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(C(=O)C[N@]1CC[N@@](C)CC1)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1) `ZINC001542877497.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001542877497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001542877497 none CN(C(=O)C[N@]1CC[N@@](C)CC1)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 10, 17, 22, 22, 33, 34, 34, 34, 34, 34, 34, 3, 10, 10, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 17, 17, 17, 33, 33, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 10, 10, 3, 4, 4, 4, 4, 10, 10] 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]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 784) grep: /scratch/xiaobo/418326/xbt-8058088.46/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(C(=O)C[N@]1CC[N@](C)CC1)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1) `ZINC001542877497.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001542877497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001542877497 none CN(C(=O)C[N@]1CC[N@](C)CC1)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 16, 21, 22, 33, 34, 34, 34, 34, 34, 34, 3, 10, 10, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 17, 17, 17, 33, 33, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 10, 10, 3, 4, 4, 4, 4, 10, 10] 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]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 785) grep: /scratch/xiaobo/418326/xbt-8058088.46/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(C(=O)C[N@]1CC[N@@](C)CC1)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1) `ZINC001542877497.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001542877497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001542877497 none CN(C(=O)C[N@]1CC[N@@](C)CC1)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.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.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 10, 18, 24, 24, 34, 35, 35, 35, 35, 35, 35, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 18, 18, 18, 34, 34, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 10, 10, 3, 4, 4, 4, 4, 10, 10] 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]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001542877497 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542877497 Building ZINC001542925056 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542925056' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542925056 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001542925056 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542925056/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542925056 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 786) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/786 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/786' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC(c2nc(c3ccccc3)cs2)CC1) `ZINC001542925056.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001542925056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542925056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001542925056 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC(c2nc(c3ccccc3)cs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 1, 1, 2, 3, 4, 4, 4, 4, 22, 22, 22, 31, 31, 25, 31, 31, 22, 22, 4, 4, 1, 1, 1, 1, 4, 4, 1, 4, 4, 4, 4, 4, 31, 31, 29, 31, 31, 22, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 8, 9, 10, 11, 12, 34, 37, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542925056 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542925056/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542925056 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 787) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/787 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/787' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC(c2nc(c3ccccc3)cs2)CC1) `ZINC001542925056.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001542925056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542925056/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001542925056 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC(c2nc(c3ccccc3)cs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 19, 19, 19, 38, 38, 30, 38, 38, 19, 19, 3, 3, 1, 1, 1, 1, 4, 4, 1, 3, 3, 3, 3, 3, 38, 38, 31, 38, 38, 19, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 8, 9, 10, 11, 12, 34, 37, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 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/418326/xbt-8058088.46/working/building/ZINC001542925056 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001542925056 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542925056/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542925056/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542925056 Building ZINC001542925056 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542925056' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542925056 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001542925056 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542925056/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542925056 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 786) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC(c2nc(c3ccccc3)cs2)CC1) `ZINC001542925056.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001542925056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542925056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001542925056 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC(c2nc(c3ccccc3)cs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 1, 1, 2, 3, 4, 4, 4, 4, 22, 22, 22, 31, 31, 25, 31, 31, 22, 22, 4, 4, 1, 1, 1, 1, 4, 4, 1, 4, 4, 4, 4, 4, 31, 31, 29, 31, 31, 22, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 8, 9, 10, 11, 12, 34, 37, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542925056 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542925056/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542925056 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 787) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC(c2nc(c3ccccc3)cs2)CC1) `ZINC001542925056.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001542925056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542925056/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001542925056 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC(c2nc(c3ccccc3)cs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 19, 19, 19, 38, 38, 30, 38, 38, 19, 19, 3, 3, 1, 1, 1, 1, 4, 4, 1, 3, 3, 3, 3, 3, 38, 38, 31, 38, 38, 19, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 8, 9, 10, 11, 12, 34, 37, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 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/418326/xbt-8058088.46/working/building/ZINC001542925056 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001542925056 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542925056/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542925056/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542925056 Building ZINC001542962584 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542962584' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542962584 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001542962584 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542962584/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542962584 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 788) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/788 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/788' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(S(=O)(=O)NCCN2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)CC2)cc1) `ZINC001542962584.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001542962584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542962584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001542962584 none Cc1ccc(S(=O)(=O)NCCN2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 24, 43, 43, 8, 4, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 43, 43, 43, 43, 43, 43, 43, 24, 8, 8, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 43, 43] 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: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542962584 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542962584/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542962584 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 789) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/789 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/789' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(S(=O)(=O)NCCN2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)CC2)cc1) `ZINC001542962584.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001542962584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542962584/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001542962584 none Cc1ccc(S(=O)(=O)NCCN2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 33, 50, 50, 13, 8, 4, 4, 4, 4, 4, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 33, 13, 13, 8, 8, 4, 4, 4, 4, 1, 1, 4, 4, 4, 4, 50, 50] 50 rigid atoms, others: [43, 44, 15, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542962584 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001542962584 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542962584/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542962584/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542962584 Building ZINC001542962584 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542962584' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542962584 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001542962584 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542962584/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542962584 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 788) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1ccc(S(=O)(=O)NCCN2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)CC2)cc1) `ZINC001542962584.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001542962584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542962584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001542962584 none Cc1ccc(S(=O)(=O)NCCN2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 24, 43, 43, 8, 4, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 43, 43, 43, 43, 43, 43, 43, 24, 8, 8, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 43, 43] 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: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542962584 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542962584/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542962584 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 789) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1ccc(S(=O)(=O)NCCN2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)CC2)cc1) `ZINC001542962584.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001542962584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542962584/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001542962584 none Cc1ccc(S(=O)(=O)NCCN2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 33, 50, 50, 13, 8, 4, 4, 4, 4, 4, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 33, 13, 13, 8, 8, 4, 4, 4, 4, 1, 1, 4, 4, 4, 4, 50, 50] 50 rigid atoms, others: [43, 44, 15, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542962584 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001542962584 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542962584/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542962584/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001542962584 Building ZINC001543706438 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001543706438' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001543706438 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001543706438 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001543706438/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001543706438 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 790) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/790 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/790' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(NS(=O)(=O)c2ccc(F)cc2)CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001543706438.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001543706438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001543706438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001543706438 none O=C(N1CCC(NS(=O)(=O)c2ccc(F)cc2)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 4, 7, 6, 6, 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, 5, 5, 5, 5, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 5, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 12, 34, 34, 34, 34, 5, 5, 5, 5, 2, 2, 2, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001543706438 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001543706438/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001543706438 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 791) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/791 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/791' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(NS(=O)(=O)c2ccc(F)cc2)CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001543706438.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001543706438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001543706438/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001543706438 none O=C(N1CCC(NS(=O)(=O)c2ccc(F)cc2)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 4, 7, 6, 6, 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, 4, 4, 4, 4, 11, 32, 32, 32, 32, 32, 32, 32, 32, 32, 4, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 11, 32, 32, 32, 32, 4, 4, 4, 4, 2, 2, 2, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001543706438 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001543706438 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001543706438/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001543706438/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001543706438 Building ZINC001543706438 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001543706438' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001543706438 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001543706438 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001543706438/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001543706438 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 790) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: O=C(N1CCC(NS(=O)(=O)c2ccc(F)cc2)CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001543706438.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001543706438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001543706438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001543706438 none O=C(N1CCC(NS(=O)(=O)c2ccc(F)cc2)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 4, 7, 6, 6, 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, 5, 5, 5, 5, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 5, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 12, 34, 34, 34, 34, 5, 5, 5, 5, 2, 2, 2, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001543706438 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001543706438/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001543706438 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 791) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: O=C(N1CCC(NS(=O)(=O)c2ccc(F)cc2)CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001543706438.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001543706438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001543706438/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001543706438 none O=C(N1CCC(NS(=O)(=O)c2ccc(F)cc2)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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 4, 7, 6, 6, 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, 4, 4, 4, 4, 11, 32, 32, 32, 32, 32, 32, 32, 32, 32, 4, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 11, 32, 32, 32, 32, 4, 4, 4, 4, 2, 2, 2, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001543706438 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001543706438 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001543706438/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001543706438/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001543706438 Building ZINC001544524868 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001544524868' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001544524868 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001544524868 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001544524868/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001544524868 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 792) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/792 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/792' -> `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(Cc1cccnc1)[C@H]1CCS(=O)(=O)C1) `ZINC001544524868.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001544524868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001544524868/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001544524868 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(Cc1cccnc1)[C@H]1CCS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 1, 5, 7, 5, 5, 14, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 1, 1, 1, 1, 3, 3, 6, 12, 27, 27, 27, 27, 27, 6, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 10, 10, 5, 10, 10, 3, 3, 3, 12, 12, 27, 27, 27, 27, 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]) total number of confs: 107 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001544524868 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001544524868/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001544524868 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 793) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/793 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/793' -> `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(Cc1cccnc1)[C@H]1CCS(=O)(=O)C1) `ZINC001544524868.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001544524868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001544524868/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001544524868 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(Cc1cccnc1)[C@H]1CCS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 1, 5, 7, 5, 5, 14, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 1, 1, 1, 1, 3, 3, 6, 11, 26, 26, 26, 26, 26, 6, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 3, 11, 11, 26, 26, 26, 26, 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]) total number of confs: 97 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001544524868 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001544524868 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001544524868/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001544524868/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001544524868 Building ZINC001544524868 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001544524868' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001544524868 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001544524868 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001544524868/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001544524868 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 792) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(Cc1cccnc1)[C@H]1CCS(=O)(=O)C1) `ZINC001544524868.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001544524868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001544524868/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001544524868 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(Cc1cccnc1)[C@H]1CCS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 1, 5, 7, 5, 5, 14, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 1, 1, 1, 1, 3, 3, 6, 12, 27, 27, 27, 27, 27, 6, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 10, 10, 5, 10, 10, 3, 3, 3, 12, 12, 27, 27, 27, 27, 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]) total number of confs: 107 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001544524868 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001544524868/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001544524868 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 793) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(Cc1cccnc1)[C@H]1CCS(=O)(=O)C1) `ZINC001544524868.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001544524868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001544524868/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001544524868 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(Cc1cccnc1)[C@H]1CCS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 1, 5, 7, 5, 5, 14, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 1, 1, 1, 1, 3, 3, 6, 11, 26, 26, 26, 26, 26, 6, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 3, 11, 11, 26, 26, 26, 26, 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]) total number of confs: 97 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001544524868 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001544524868 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001544524868/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001544524868/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001544524868 Building ZINC001544524899 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001544524899' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001544524899 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001544524899 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001544524899/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001544524899 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 794) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/794 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/794' -> `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(Cc1cccnc1)[C@@H]1CCS(=O)(=O)C1) `ZINC001544524899.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001544524899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001544524899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001544524899 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(Cc1cccnc1)[C@@H]1CCS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 1, 5, 7, 5, 5, 14, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 6, 10, 10, 3, 3, 1, 1, 1, 1, 3, 3, 5, 11, 27, 27, 27, 27, 27, 5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 10, 10, 7, 10, 10, 3, 3, 3, 11, 11, 27, 27, 27, 27, 7, 7, 7, 7, 7, 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, 51, 52, 53, 54, 55]) total number of confs: 100 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001544524899 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001544524899/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001544524899 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 795) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/795 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/795' -> `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(Cc1cccnc1)[C@@H]1CCS(=O)(=O)C1) `ZINC001544524899.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001544524899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001544524899/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001544524899 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(Cc1cccnc1)[C@@H]1CCS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 1, 5, 7, 5, 5, 14, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 2, 2, 4, 9, 25, 25, 25, 25, 25, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 9, 9, 25, 25, 25, 25, 7, 7, 7, 7, 7, 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, 51, 52, 53, 54, 55]) total number of confs: 88 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001544524899 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001544524899 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001544524899/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001544524899/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001544524899 Building ZINC001544524899 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001544524899' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001544524899 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001544524899 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001544524899/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001544524899 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 794) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(Cc1cccnc1)[C@@H]1CCS(=O)(=O)C1) `ZINC001544524899.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001544524899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001544524899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001544524899 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(Cc1cccnc1)[C@@H]1CCS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 1, 5, 7, 5, 5, 14, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 6, 10, 10, 3, 3, 1, 1, 1, 1, 3, 3, 5, 11, 27, 27, 27, 27, 27, 5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 10, 10, 7, 10, 10, 3, 3, 3, 11, 11, 27, 27, 27, 27, 7, 7, 7, 7, 7, 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, 51, 52, 53, 54, 55]) total number of confs: 100 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001544524899 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001544524899/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001544524899 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 795) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(Cc1cccnc1)[C@@H]1CCS(=O)(=O)C1) `ZINC001544524899.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001544524899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001544524899/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001544524899 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(Cc1cccnc1)[C@@H]1CCS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 1, 5, 7, 5, 5, 14, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 2, 2, 4, 9, 25, 25, 25, 25, 25, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 9, 9, 25, 25, 25, 25, 7, 7, 7, 7, 7, 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, 51, 52, 53, 54, 55]) total number of confs: 88 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001544524899 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001544524899 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001544524899/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001544524899/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001544524899 Building ZINC001545877330 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001545877330' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001545877330 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001545877330 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001545877330/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001545877330 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 796) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/796 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/796' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCS(=O)(=O)C1) `ZINC001545877330.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001545877330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001545877330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001545877330 none CCN(CC)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 14, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 11, 17, 26, 10, 6, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 6, 9, 9, 9, 9, 9, 9, 9, 28, 28, 28, 28, 28, 26, 26, 26, 26, 26, 11, 11, 10, 10, 8, 8, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 189 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001545877330 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001545877330/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001545877330 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 797) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/797 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/797' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCS(=O)(=O)C1) `ZINC001545877330.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001545877330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001545877330/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001545877330 none CCN(CC)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 14, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 11, 19, 26, 11, 7, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 7, 9, 9, 9, 9, 9, 9, 9, 25, 25, 25, 25, 25, 26, 26, 26, 26, 26, 11, 11, 11, 11, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 157 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001545877330 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001545877330 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001545877330/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001545877330/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001545877330 Building ZINC001545877330 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001545877330' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001545877330 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001545877330 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001545877330/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001545877330 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 796) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCN(CC)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCS(=O)(=O)C1) `ZINC001545877330.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001545877330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001545877330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001545877330 none CCN(CC)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 14, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 11, 17, 26, 10, 6, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 6, 9, 9, 9, 9, 9, 9, 9, 28, 28, 28, 28, 28, 26, 26, 26, 26, 26, 11, 11, 10, 10, 8, 8, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 189 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001545877330 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001545877330/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001545877330 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 797) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCN(CC)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCS(=O)(=O)C1) `ZINC001545877330.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001545877330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001545877330/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001545877330 none CCN(CC)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 14, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 11, 19, 26, 11, 7, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 7, 9, 9, 9, 9, 9, 9, 9, 25, 25, 25, 25, 25, 26, 26, 26, 26, 26, 11, 11, 11, 11, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 157 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001545877330 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001545877330 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001545877330/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001545877330/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001545877330 Building ZINC001545877331 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001545877331' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001545877331 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001545877331 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001545877331/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001545877331 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 798) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/798 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/798' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCS(=O)(=O)C1) `ZINC001545877331.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001545877331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001545877331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001545877331 none CCN(CC)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 14, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 20, 12, 20, 24, 10, 7, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 7, 10, 10, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 24, 24, 24, 24, 24, 12, 12, 10, 10, 8, 8, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 145 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001545877331 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001545877331/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001545877331 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 799) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/799 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/799' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCS(=O)(=O)C1) `ZINC001545877331.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001545877331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001545877331/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001545877331 none CCN(CC)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 14, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 20, 28, 11, 6, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 6, 12, 12, 12, 12, 12, 12, 12, 27, 27, 27, 27, 27, 28, 28, 28, 28, 28, 12, 12, 11, 11, 5, 5, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 186 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001545877331 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001545877331 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001545877331/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001545877331/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001545877331 Building ZINC001545877331 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001545877331' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001545877331 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001545877331 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001545877331/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001545877331 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 798) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCN(CC)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCS(=O)(=O)C1) `ZINC001545877331.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001545877331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001545877331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001545877331 none CCN(CC)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 14, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 20, 12, 20, 24, 10, 7, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 7, 10, 10, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 24, 24, 24, 24, 24, 12, 12, 10, 10, 8, 8, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 145 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001545877331 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001545877331/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001545877331 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 799) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCN(CC)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCS(=O)(=O)C1) `ZINC001545877331.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001545877331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001545877331/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001545877331 none CCN(CC)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 14, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 20, 28, 11, 6, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 6, 12, 12, 12, 12, 12, 12, 12, 27, 27, 27, 27, 27, 28, 28, 28, 28, 28, 12, 12, 11, 11, 5, 5, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 186 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001545877331 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001545877331 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001545877331/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001545877331/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001545877331 Building ZINC001546130608 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546130608' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546130608 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001546130608 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546130608/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546130608 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 800) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/800 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/800' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN([C@H]3CCCN(Cc4ccccc4)C3=O)CC2)cn1) `ZINC001546130608.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001546130608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546130608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 69 natoms 68 natoms 67 natoms 66 names: ZINC001546130608 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN([C@H]3CCCN(Cc4ccccc4)C3=O)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', 'N.3', 'C.3', 'H', 'C.3', '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', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 2, 2, 1, 1, 1, 1, 2, 4, 6, 6, 6, 10, 14, 14, 14, 14, 14, 14, 33, 36, 36, 35, 36, 36, 14, 14, 6, 6, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 33, 33, 36, 36, 35, 36, 36, 6, 6, 6, 6, 2] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 147 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546130608 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546130608/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546130608 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 801) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/801 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/801' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN([C@H]3CCCN(Cc4ccccc4)C3=O)CC2)cn1) `ZINC001546130608.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001546130608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546130608/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 69 natoms 68 natoms 67 natoms 66 names: ZINC001546130608 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN([C@H]3CCCN(Cc4ccccc4)C3=O)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', 'N.3', 'C.3', 'H', 'C.3', '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', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 2, 2, 1, 1, 1, 1, 2, 2, 3, 3, 3, 8, 12, 12, 12, 12, 12, 12, 30, 36, 36, 33, 36, 36, 12, 12, 3, 3, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 30, 30, 36, 36, 33, 36, 36, 3, 3, 3, 3, 2] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 151 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546130608 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001546130608 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546130608/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546130608/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546130608 Building ZINC001546130608 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546130608' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546130608 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001546130608 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546130608/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546130608 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 800) grep: /scratch/xiaobo/418326/xbt-8058088.46/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)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN([C@H]3CCCN(Cc4ccccc4)C3=O)CC2)cn1) `ZINC001546130608.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001546130608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546130608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 69 natoms 68 natoms 67 natoms 66 names: ZINC001546130608 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN([C@H]3CCCN(Cc4ccccc4)C3=O)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', 'N.3', 'C.3', 'H', 'C.3', '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', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 2, 2, 1, 1, 1, 1, 2, 4, 6, 6, 6, 10, 14, 14, 14, 14, 14, 14, 33, 36, 36, 35, 36, 36, 14, 14, 6, 6, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 33, 33, 36, 36, 35, 36, 36, 6, 6, 6, 6, 2] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 147 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546130608 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546130608/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546130608 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 801) grep: /scratch/xiaobo/418326/xbt-8058088.46/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)n1cc([C@]([O-])([SiH3])C(=O)N2CCN([C@H]3CCCN(Cc4ccccc4)C3=O)CC2)cn1) `ZINC001546130608.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001546130608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546130608/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 69 natoms 68 natoms 67 natoms 66 names: ZINC001546130608 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN([C@H]3CCCN(Cc4ccccc4)C3=O)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', 'N.3', 'C.3', 'H', 'C.3', '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', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 2, 2, 1, 1, 1, 1, 2, 2, 3, 3, 3, 8, 12, 12, 12, 12, 12, 12, 30, 36, 36, 33, 36, 36, 12, 12, 3, 3, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 30, 30, 36, 36, 33, 36, 36, 3, 3, 3, 3, 2] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 151 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546130608 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001546130608 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546130608/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546130608/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546130608 Building ZINC001546130609 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546130609' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546130609 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001546130609 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546130609/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546130609 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 802) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/802 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/802' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN([C@@H]3CCCN(Cc4ccccc4)C3=O)CC2)cn1) `ZINC001546130609.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001546130609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546130609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 69 natoms 68 natoms 67 natoms 66 names: ZINC001546130609 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN([C@@H]3CCCN(Cc4ccccc4)C3=O)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', 'N.3', 'C.3', 'H', 'C.3', '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', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 2, 2, 1, 1, 1, 1, 2, 4, 7, 7, 7, 9, 14, 14, 14, 14, 14, 14, 32, 38, 38, 32, 38, 38, 14, 14, 7, 7, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 7, 7, 7, 7, 14, 14, 14, 14, 14, 14, 32, 32, 38, 38, 32, 38, 38, 7, 7, 7, 7, 2] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 166 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546130609 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546130609/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546130609 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 803) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/803 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/803' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN([C@@H]3CCCN(Cc4ccccc4)C3=O)CC2)cn1) `ZINC001546130609.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001546130609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546130609/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 69 natoms 68 natoms 67 natoms 66 names: ZINC001546130609 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN([C@@H]3CCCN(Cc4ccccc4)C3=O)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', 'N.3', 'C.3', 'H', 'C.3', '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', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 4, 4, 4, 9, 17, 17, 17, 17, 17, 17, 33, 36, 36, 33, 36, 36, 17, 17, 4, 4, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 4, 4, 4, 4, 17, 17, 17, 17, 17, 17, 33, 33, 36, 36, 33, 36, 36, 4, 4, 4, 4, 3] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 153 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546130609 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001546130609 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546130609/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546130609/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546130609 Building ZINC001546130609 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546130609' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546130609 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001546130609 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546130609/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546130609 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 802) grep: /scratch/xiaobo/418326/xbt-8058088.46/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)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN([C@@H]3CCCN(Cc4ccccc4)C3=O)CC2)cn1) `ZINC001546130609.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001546130609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546130609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 69 natoms 68 natoms 67 natoms 66 names: ZINC001546130609 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN([C@@H]3CCCN(Cc4ccccc4)C3=O)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', 'N.3', 'C.3', 'H', 'C.3', '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', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 2, 2, 1, 1, 1, 1, 2, 4, 7, 7, 7, 9, 14, 14, 14, 14, 14, 14, 32, 38, 38, 32, 38, 38, 14, 14, 7, 7, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 7, 7, 7, 7, 14, 14, 14, 14, 14, 14, 32, 32, 38, 38, 32, 38, 38, 7, 7, 7, 7, 2] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 166 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546130609 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546130609/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546130609 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 803) grep: /scratch/xiaobo/418326/xbt-8058088.46/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)n1cc([C@]([O-])([SiH3])C(=O)N2CCN([C@@H]3CCCN(Cc4ccccc4)C3=O)CC2)cn1) `ZINC001546130609.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001546130609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546130609/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 69 natoms 68 natoms 67 natoms 66 names: ZINC001546130609 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN([C@@H]3CCCN(Cc4ccccc4)C3=O)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', 'N.3', 'C.3', 'H', 'C.3', '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', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 4, 4, 4, 9, 17, 17, 17, 17, 17, 17, 33, 36, 36, 33, 36, 36, 17, 17, 4, 4, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 4, 4, 4, 4, 17, 17, 17, 17, 17, 17, 33, 33, 36, 36, 33, 36, 36, 4, 4, 4, 4, 3] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 153 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546130609 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001546130609 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546130609/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546130609/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546130609 Building ZINC001546175001 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546175001' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546175001 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001546175001 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546175001/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546175001 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 804) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/804 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/804' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H](c1cccc(C(F)(F)F)c1)C(F)(F)F) `ZINC001546175001.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001546175001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546175001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001546175001 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H](c1cccc(C(F)(F)F)c1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 3, 1, 1, 1, 1, 3, 3, 3, 6, 6, 14, 14, 11, 14, 14, 14, 14, 14, 14, 6, 6, 6, 6, 3, 3, 3, 3, 8, 8, 3, 3, 14, 14, 12, 14] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546175001 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546175001/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546175001 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 805) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/805 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/805' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H](c1cccc(C(F)(F)F)c1)C(F)(F)F) `ZINC001546175001.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001546175001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546175001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001546175001 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H](c1cccc(C(F)(F)F)c1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 14, 14, 9, 14, 14, 14, 14, 14, 14, 5, 5, 5, 5, 3, 3, 3, 3, 7, 7, 3, 3, 14, 14, 9, 14] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 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: 66 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546175001 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001546175001 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546175001/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546175001/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546175001 Building ZINC001546175001 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546175001' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546175001 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001546175001 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546175001/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546175001 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 804) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H](c1cccc(C(F)(F)F)c1)C(F)(F)F) `ZINC001546175001.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001546175001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546175001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001546175001 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H](c1cccc(C(F)(F)F)c1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 3, 1, 1, 1, 1, 3, 3, 3, 6, 6, 14, 14, 11, 14, 14, 14, 14, 14, 14, 6, 6, 6, 6, 3, 3, 3, 3, 8, 8, 3, 3, 14, 14, 12, 14] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546175001 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546175001/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546175001 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 805) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H](c1cccc(C(F)(F)F)c1)C(F)(F)F) `ZINC001546175001.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001546175001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546175001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001546175001 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H](c1cccc(C(F)(F)F)c1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 14, 14, 9, 14, 14, 14, 14, 14, 14, 5, 5, 5, 5, 3, 3, 3, 3, 7, 7, 3, 3, 14, 14, 9, 14] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 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: 66 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546175001 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001546175001 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546175001/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546175001/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546175001 Building ZINC001546175002 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546175002' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546175002 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001546175002 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546175002/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546175002 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 806) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/806 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/806' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1cccc(C(F)(F)F)c1)C(F)(F)F) `ZINC001546175002.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001546175002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546175002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001546175002 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1cccc(C(F)(F)F)c1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 14, 14, 9, 14, 14, 14, 14, 14, 14, 5, 5, 5, 5, 3, 3, 3, 3, 7, 7, 3, 3, 14, 14, 9, 14] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 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: 66 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546175002 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546175002/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546175002 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 807) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/807 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/807' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H](c1cccc(C(F)(F)F)c1)C(F)(F)F) `ZINC001546175002.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001546175002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546175002/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001546175002 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H](c1cccc(C(F)(F)F)c1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 8, 4, 1, 1, 1, 1, 3, 3, 3, 6, 6, 14, 14, 11, 14, 14, 14, 14, 14, 14, 6, 6, 6, 6, 4, 4, 4, 4, 8, 8, 4, 3, 14, 14, 12, 14] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 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: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546175002 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001546175002 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546175002/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546175002/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546175002 Building ZINC001546175002 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546175002' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546175002 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001546175002 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546175002/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546175002 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 806) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1cccc(C(F)(F)F)c1)C(F)(F)F) `ZINC001546175002.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001546175002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546175002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001546175002 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1cccc(C(F)(F)F)c1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 14, 14, 9, 14, 14, 14, 14, 14, 14, 5, 5, 5, 5, 3, 3, 3, 3, 7, 7, 3, 3, 14, 14, 9, 14] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 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: 66 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546175002 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546175002/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546175002 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 807) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H](c1cccc(C(F)(F)F)c1)C(F)(F)F) `ZINC001546175002.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001546175002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546175002/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001546175002 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H](c1cccc(C(F)(F)F)c1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 8, 4, 1, 1, 1, 1, 3, 3, 3, 6, 6, 14, 14, 11, 14, 14, 14, 14, 14, 14, 6, 6, 6, 6, 4, 4, 4, 4, 8, 8, 4, 3, 14, 14, 12, 14] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 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: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546175002 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001546175002 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546175002/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546175002/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001546175002 Building ZINC001556088606 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556088606' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556088606 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001556088606 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556088606/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556088606 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 808) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/808 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/808' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1Cc2cc(c3ccc(CNC(=O)[C@@]([O-])([SiH3])c4cc(S(N)(=O)=O)cn4C)cc3)ccc2O1) `ZINC001556088606.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001556088606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556088606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001556088606 none C[C@H]1Cc2cc(c3ccc(CNC(=O)[C@@]([O-])([SiH3])c4cc(S(N)(=O)=O)cn4C)cc3)ccc2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', '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, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 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: [36, 36, 36, 36, 36, 36, 25, 7, 25, 25, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 25, 25, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 25, 25, 7, 7, 2, 1, 3, 3, 1, 1, 1, 1, 25, 25, 36, 36] 50 rigid atoms, others: [48, 50, 49, 44, 13, 15, 16, 17, 18, 19, 20, 24, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 51, 52, 53, 54]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556088606 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556088606/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556088606 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 809) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/809 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/809' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1Cc2cc(c3ccc(CNC(=O)[C@]([O-])([SiH3])c4cc(S(N)(=O)=O)cn4C)cc3)ccc2O1) `ZINC001556088606.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001556088606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556088606/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001556088606 none C[C@H]1Cc2cc(c3ccc(CNC(=O)[C@]([O-])([SiH3])c4cc(S(N)(=O)=O)cn4C)cc3)ccc2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', '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, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 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: [35, 35, 35, 35, 35, 35, 25, 14, 25, 25, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 25, 25, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 25, 25, 7, 7, 2, 1, 3, 3, 1, 1, 1, 1, 25, 25, 35, 35] 50 rigid atoms, others: [48, 50, 49, 44, 13, 15, 16, 17, 18, 19, 20, 24, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 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/418326/xbt-8058088.46/working/building/ZINC001556088606 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001556088606 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556088606/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556088606/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556088606 Building ZINC001556088606 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556088606' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556088606 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001556088606 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556088606/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556088606 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 808) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: C[C@H]1Cc2cc(c3ccc(CNC(=O)[C@@]([O-])([SiH3])c4cc(S(N)(=O)=O)cn4C)cc3)ccc2O1) `ZINC001556088606.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001556088606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556088606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001556088606 none C[C@H]1Cc2cc(c3ccc(CNC(=O)[C@@]([O-])([SiH3])c4cc(S(N)(=O)=O)cn4C)cc3)ccc2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', '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, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 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: [36, 36, 36, 36, 36, 36, 25, 7, 25, 25, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 25, 25, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 25, 25, 7, 7, 2, 1, 3, 3, 1, 1, 1, 1, 25, 25, 36, 36] 50 rigid atoms, others: [48, 50, 49, 44, 13, 15, 16, 17, 18, 19, 20, 24, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 51, 52, 53, 54]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556088606 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556088606/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556088606 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 809) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: C[C@H]1Cc2cc(c3ccc(CNC(=O)[C@]([O-])([SiH3])c4cc(S(N)(=O)=O)cn4C)cc3)ccc2O1) `ZINC001556088606.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001556088606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556088606/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001556088606 none C[C@H]1Cc2cc(c3ccc(CNC(=O)[C@]([O-])([SiH3])c4cc(S(N)(=O)=O)cn4C)cc3)ccc2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', '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, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 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: [35, 35, 35, 35, 35, 35, 25, 14, 25, 25, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 25, 25, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 25, 25, 7, 7, 2, 1, 3, 3, 1, 1, 1, 1, 25, 25, 35, 35] 50 rigid atoms, others: [48, 50, 49, 44, 13, 15, 16, 17, 18, 19, 20, 24, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 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/418326/xbt-8058088.46/working/building/ZINC001556088606 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001556088606 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556088606/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556088606/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556088606 Building ZINC001556088607 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556088607' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556088607 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001556088607 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556088607/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556088607 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 810) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/810 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/810' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1Cc2cc(c3ccc(CNC(=O)[C@@]([O-])([SiH3])c4cc(S(N)(=O)=O)cn4C)cc3)ccc2O1) `ZINC001556088607.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001556088607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556088607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001556088607 none C[C@@H]1Cc2cc(c3ccc(CNC(=O)[C@@]([O-])([SiH3])c4cc(S(N)(=O)=O)cn4C)cc3)ccc2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', '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, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 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: [35, 35, 35, 35, 35, 35, 25, 14, 25, 25, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 25, 25, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 25, 25, 7, 7, 2, 1, 3, 3, 1, 1, 1, 1, 25, 25, 35, 35] 50 rigid atoms, others: [48, 50, 49, 44, 13, 15, 16, 17, 18, 19, 20, 24, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 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/418326/xbt-8058088.46/working/building/ZINC001556088607 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556088607/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556088607 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 811) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/811 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/811' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1Cc2cc(c3ccc(CNC(=O)[C@]([O-])([SiH3])c4cc(S(N)(=O)=O)cn4C)cc3)ccc2O1) `ZINC001556088607.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001556088607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556088607/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001556088607 none C[C@@H]1Cc2cc(c3ccc(CNC(=O)[C@]([O-])([SiH3])c4cc(S(N)(=O)=O)cn4C)cc3)ccc2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', '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, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 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: [36, 36, 36, 36, 36, 36, 25, 7, 25, 25, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 25, 25, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 25, 25, 7, 7, 2, 1, 3, 3, 1, 1, 1, 1, 25, 25, 36, 36] 50 rigid atoms, others: [48, 50, 49, 44, 13, 15, 16, 17, 18, 19, 20, 24, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 51, 52, 53, 54]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556088607 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001556088607 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556088607/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556088607/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556088607 Building ZINC001556088607 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556088607' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556088607 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001556088607 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556088607/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556088607 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 810) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: C[C@@H]1Cc2cc(c3ccc(CNC(=O)[C@@]([O-])([SiH3])c4cc(S(N)(=O)=O)cn4C)cc3)ccc2O1) `ZINC001556088607.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001556088607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556088607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001556088607 none C[C@@H]1Cc2cc(c3ccc(CNC(=O)[C@@]([O-])([SiH3])c4cc(S(N)(=O)=O)cn4C)cc3)ccc2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', '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, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 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: [35, 35, 35, 35, 35, 35, 25, 14, 25, 25, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 25, 25, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 25, 25, 7, 7, 2, 1, 3, 3, 1, 1, 1, 1, 25, 25, 35, 35] 50 rigid atoms, others: [48, 50, 49, 44, 13, 15, 16, 17, 18, 19, 20, 24, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 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/418326/xbt-8058088.46/working/building/ZINC001556088607 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556088607/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556088607 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 811) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: C[C@@H]1Cc2cc(c3ccc(CNC(=O)[C@]([O-])([SiH3])c4cc(S(N)(=O)=O)cn4C)cc3)ccc2O1) `ZINC001556088607.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001556088607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556088607/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001556088607 none C[C@@H]1Cc2cc(c3ccc(CNC(=O)[C@]([O-])([SiH3])c4cc(S(N)(=O)=O)cn4C)cc3)ccc2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', '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, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 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: [36, 36, 36, 36, 36, 36, 25, 7, 25, 25, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 25, 25, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 25, 25, 7, 7, 2, 1, 3, 3, 1, 1, 1, 1, 25, 25, 36, 36] 50 rigid atoms, others: [48, 50, 49, 44, 13, 15, 16, 17, 18, 19, 20, 24, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 51, 52, 53, 54]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556088607 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001556088607 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556088607/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556088607/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556088607 Building ZINC001556260554 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556260554' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556260554 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001556260554 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556260554/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556260554 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 812) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/812 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/812' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](Cc1ccccc1Br)N(C)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001556260554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001556260554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556260554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001556260554 none CC[C@H](Cc1ccccc1Br)N(C)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 8, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 2, 4, 4, 10, 14, 14, 10, 14, 14, 14, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 7, 7, 7, 2, 2, 2, 5, 5, 5, 5, 5, 10, 10, 14, 14, 14, 14, 2, 2, 2, 2, 7, 7, 2, 2, 2, 2] 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: 101 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556260554 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556260554/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556260554 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 813) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/813 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/813' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](Cc1ccccc1Br)N(C)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001556260554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001556260554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556260554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001556260554 none CC[C@H](Cc1ccccc1Br)N(C)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 8, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 3, 5, 5, 9, 14, 14, 9, 14, 14, 14, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 6, 6, 6, 6, 6, 9, 9, 14, 14, 14, 14, 3, 3, 3, 2, 5, 5, 2, 2, 2, 2] 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: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556260554 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001556260554 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556260554/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556260554/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556260554 Building ZINC001556260554 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556260554' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556260554 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001556260554 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556260554/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556260554 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 812) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC[C@H](Cc1ccccc1Br)N(C)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001556260554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001556260554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556260554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001556260554 none CC[C@H](Cc1ccccc1Br)N(C)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 8, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 2, 4, 4, 10, 14, 14, 10, 14, 14, 14, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 7, 7, 7, 2, 2, 2, 5, 5, 5, 5, 5, 10, 10, 14, 14, 14, 14, 2, 2, 2, 2, 7, 7, 2, 2, 2, 2] 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: 101 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556260554 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556260554/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556260554 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 813) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC[C@H](Cc1ccccc1Br)N(C)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001556260554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001556260554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556260554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001556260554 none CC[C@H](Cc1ccccc1Br)N(C)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 8, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 3, 5, 5, 9, 14, 14, 9, 14, 14, 14, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 6, 6, 6, 6, 6, 9, 9, 14, 14, 14, 14, 3, 3, 3, 2, 5, 5, 2, 2, 2, 2] 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: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556260554 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001556260554 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556260554/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556260554/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556260554 Building ZINC001556260555 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556260555' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556260555 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001556260555 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556260555/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556260555 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 814) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/814 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/814' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](Cc1ccccc1Br)N(C)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001556260555.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001556260555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556260555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001556260555 none CC[C@@H](Cc1ccccc1Br)N(C)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 8, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 3, 5, 5, 9, 14, 14, 9, 14, 14, 14, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 6, 6, 6, 6, 6, 9, 9, 14, 14, 14, 14, 3, 3, 3, 2, 5, 5, 2, 2, 2, 2] 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: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556260555 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556260555/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556260555 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 815) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/815 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/815' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](Cc1ccccc1Br)N(C)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001556260555.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001556260555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556260555/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001556260555 none CC[C@@H](Cc1ccccc1Br)N(C)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 8, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 2, 4, 4, 10, 14, 14, 10, 14, 14, 14, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 7, 7, 7, 2, 2, 2, 5, 5, 5, 5, 5, 10, 10, 14, 14, 14, 14, 2, 2, 2, 2, 7, 7, 2, 2, 2, 2] 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: 101 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556260555 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001556260555 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556260555/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556260555/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556260555 Building ZINC001556260555 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556260555' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556260555 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001556260555 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556260555/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556260555 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 814) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC[C@@H](Cc1ccccc1Br)N(C)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001556260555.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001556260555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556260555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001556260555 none CC[C@@H](Cc1ccccc1Br)N(C)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 8, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 3, 5, 5, 9, 14, 14, 9, 14, 14, 14, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 6, 6, 6, 6, 6, 9, 9, 14, 14, 14, 14, 3, 3, 3, 2, 5, 5, 2, 2, 2, 2] 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: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556260555 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556260555/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556260555 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 815) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC[C@@H](Cc1ccccc1Br)N(C)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001556260555.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001556260555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556260555/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001556260555 none CC[C@@H](Cc1ccccc1Br)N(C)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 8, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 2, 4, 4, 10, 14, 14, 10, 14, 14, 14, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 7, 7, 7, 2, 2, 2, 5, 5, 5, 5, 5, 10, 10, 14, 14, 14, 14, 2, 2, 2, 2, 7, 7, 2, 2, 2, 2] 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: 101 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556260555 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001556260555 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556260555/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556260555/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556260555 Building ZINC001556808030 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556808030' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556808030 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001556808030 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556808030/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556808030 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 816) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/816 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/816' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC(c2ccc(OC(F)(F)F)cc2)CC1) `ZINC001556808030.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001556808030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556808030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001556808030 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC(c2ccc(OC(F)(F)F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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', 'H', 'H', 'H', '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, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 1, 1, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 18, 18, 18, 18, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 8, 9, 10, 11, 12, 34, 37, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556808030 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556808030/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556808030 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 817) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/817 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/817' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC(c2ccc(OC(F)(F)F)cc2)CC1) `ZINC001556808030.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001556808030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556808030/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001556808030 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC(c2ccc(OC(F)(F)F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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', 'H', 'H', 'H', '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, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 7, 7, 3, 5, 28, 27, 28, 28, 7, 7, 3, 3, 1, 1, 1, 1, 4, 4, 1, 3, 3, 3, 3, 3, 7, 7, 7, 7, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 8, 9, 10, 11, 34, 37, 31] set([5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556808030 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001556808030 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556808030/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556808030/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556808030 Building ZINC001556808030 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556808030' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556808030 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001556808030 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556808030/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556808030 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 816) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC(c2ccc(OC(F)(F)F)cc2)CC1) `ZINC001556808030.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001556808030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556808030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001556808030 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC(c2ccc(OC(F)(F)F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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', 'H', 'H', 'H', '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, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 1, 1, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 18, 18, 18, 18, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 8, 9, 10, 11, 12, 34, 37, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556808030 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556808030/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556808030 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 817) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC(c2ccc(OC(F)(F)F)cc2)CC1) `ZINC001556808030.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001556808030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556808030/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001556808030 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC(c2ccc(OC(F)(F)F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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', 'H', 'H', 'H', '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, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 7, 7, 3, 5, 28, 27, 28, 28, 7, 7, 3, 3, 1, 1, 1, 1, 4, 4, 1, 3, 3, 3, 3, 3, 7, 7, 7, 7, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 8, 9, 10, 11, 34, 37, 31] set([5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556808030 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001556808030 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556808030/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556808030/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001556808030 Building ZINC001557125006 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557125006' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557125006 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001557125006 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557125006/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557125006 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 818) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/818 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/818' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(CN3CCS(=O)(=O)CC3)cc2)cc1Cl) `ZINC001557125006.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001557125006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557125006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001557125006 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(CN3CCS(=O)(=O)CC3)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.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 10, 5, 5, 14, 11, 11, 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] 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, 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, 7, 7] 0 hydrogens need 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, 5, 10, 10, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 10, 10, 2, 2, 2, 4, 4, 4, 2, 2, 1, 5, 5, 10, 10, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 10, 10, 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, 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/418326/xbt-8058088.46/working/building/ZINC001557125006 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557125006/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557125006 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 819) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/819 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/819' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(CN3CCS(=O)(=O)CC3)cc2)cc1Cl) `ZINC001557125006.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001557125006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557125006/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001557125006 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(CN3CCS(=O)(=O)CC3)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.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 10, 5, 5, 14, 11, 11, 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] 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, 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, 7, 7] 0 hydrogens need 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, 5, 10, 10, 5, 5, 28, 28, 28, 28, 28, 28, 28, 28, 10, 10, 2, 2, 2, 4, 4, 4, 2, 2, 1, 5, 5, 10, 10, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 10, 10, 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, 52]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557125006 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001557125006 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557125006/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557125006/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557125006 Building ZINC001557125006 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557125006' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557125006 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001557125006 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557125006/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557125006 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 818) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(CN3CCS(=O)(=O)CC3)cc2)cc1Cl) `ZINC001557125006.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001557125006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557125006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001557125006 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(CN3CCS(=O)(=O)CC3)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.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 10, 5, 5, 14, 11, 11, 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] 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, 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, 7, 7] 0 hydrogens need 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, 5, 10, 10, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 10, 10, 2, 2, 2, 4, 4, 4, 2, 2, 1, 5, 5, 10, 10, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 10, 10, 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, 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/418326/xbt-8058088.46/working/building/ZINC001557125006 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557125006/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557125006 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 819) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(CN3CCS(=O)(=O)CC3)cc2)cc1Cl) `ZINC001557125006.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001557125006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557125006/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001557125006 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(CN3CCS(=O)(=O)CC3)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.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 10, 5, 5, 14, 11, 11, 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] 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, 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, 7, 7] 0 hydrogens need 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, 5, 10, 10, 5, 5, 28, 28, 28, 28, 28, 28, 28, 28, 10, 10, 2, 2, 2, 4, 4, 4, 2, 2, 1, 5, 5, 10, 10, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 10, 10, 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, 52]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557125006 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001557125006 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557125006/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557125006/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557125006 Building ZINC001557146743 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557146743' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557146743 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001557146743 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557146743/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557146743 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 820) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/820 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/820' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(SCCN2CCCCC2)cc1) `ZINC001557146743.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001557146743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557146743/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001557146743 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(SCCN2CCCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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.3', 'N.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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 5, 5, 10, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 4, 5, 9, 9, 9, 18, 18, 18, 18, 18, 5, 5, 1, 1, 1, 1, 4, 4, 1, 2, 5, 5, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 8, 9, 10, 11, 12, 36, 30, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 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: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557146743 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557146743/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557146743 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 821) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/821 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/821' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(SCCN2CCCCC2)cc1) `ZINC001557146743.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001557146743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557146743/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001557146743 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(SCCN2CCCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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.3', 'N.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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 5, 5, 10, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 2, 2, 9, 9, 9, 18, 18, 18, 18, 18, 5, 5, 1, 1, 1, 1, 4, 4, 1, 2, 5, 5, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 8, 9, 10, 11, 12, 36, 30, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 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: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557146743 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001557146743 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557146743/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557146743/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557146743 Building ZINC001557146743 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557146743' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557146743 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001557146743 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557146743/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557146743 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 820) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(SCCN2CCCCC2)cc1) `ZINC001557146743.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001557146743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557146743/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001557146743 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(SCCN2CCCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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.3', 'N.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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 5, 5, 10, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 4, 5, 9, 9, 9, 18, 18, 18, 18, 18, 5, 5, 1, 1, 1, 1, 4, 4, 1, 2, 5, 5, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 8, 9, 10, 11, 12, 36, 30, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 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: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557146743 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557146743/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557146743 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 821) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(SCCN2CCCCC2)cc1) `ZINC001557146743.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001557146743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557146743/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001557146743 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(SCCN2CCCCC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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.3', 'N.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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 5, 5, 10, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 2, 2, 9, 9, 9, 18, 18, 18, 18, 18, 5, 5, 1, 1, 1, 1, 4, 4, 1, 2, 5, 5, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 8, 9, 10, 11, 12, 36, 30, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 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: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557146743 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001557146743 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557146743/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557146743/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557146743 Building ZINC001557310995 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557310995' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557310995 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001557310995 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557310995/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557310995 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 822) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/822 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/822' -> `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)N1CCc2nc[nH]c2C12CCN(C(=O)OC(C)(C)C)CC2) `ZINC001557310995.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001557310995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557310995/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001557310995 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2nc[nH]c2C12CCN(C(=O)OC(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 8, 6, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 19, 19, 40, 40, 40, 40, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 40, 40, 40, 40, 40, 40, 40, 40, 40, 9, 9, 9, 9] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 89 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557310995 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557310995/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557310995 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 823) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/823 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/823' -> `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)N1CCc2nc[nH]c2C12CCN(C(=O)OC(C)(C)C)CC2) `ZINC001557310995.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001557310995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557310995/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001557310995 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2nc[nH]c2C12CCN(C(=O)OC(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 8, 6, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 22, 22, 40, 40, 40, 40, 12, 12, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 40, 40, 40, 40, 40, 40, 40, 40, 40, 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, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 92 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557310995 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001557310995 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557310995/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557310995/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557310995 Building ZINC001557310995 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557310995' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557310995 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001557310995 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557310995/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557310995 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 822) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2nc[nH]c2C12CCN(C(=O)OC(C)(C)C)CC2) `ZINC001557310995.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001557310995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557310995/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001557310995 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2nc[nH]c2C12CCN(C(=O)OC(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 8, 6, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 19, 19, 40, 40, 40, 40, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 40, 40, 40, 40, 40, 40, 40, 40, 40, 9, 9, 9, 9] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 89 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557310995 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557310995/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557310995 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 823) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2nc[nH]c2C12CCN(C(=O)OC(C)(C)C)CC2) `ZINC001557310995.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001557310995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557310995/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001557310995 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2nc[nH]c2C12CCN(C(=O)OC(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 8, 6, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 22, 22, 40, 40, 40, 40, 12, 12, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 40, 40, 40, 40, 40, 40, 40, 40, 40, 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, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 92 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557310995 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001557310995 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557310995/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557310995/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557310995 Building ZINC001557844103 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557844103' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557844103 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001557844103 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557844103/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557844103 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 824) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/824 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/824' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCON(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H](C)c1cccc(Br)c1) `ZINC001557844103.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001557844103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557844103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001557844103 none CCON(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H](C)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 7, 7, 7, 2, 2, 2, 4, 5, 5, 5, 16, 16, 12, 16, 16, 16, 6, 6, 6, 6, 6, 2, 7, 7, 2, 2, 2, 2, 5, 5, 5, 16, 16, 12, 16] 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557844103 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557844103/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557844103 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 825) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/825 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/825' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCON(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H](C)c1cccc(Br)c1) `ZINC001557844103.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001557844103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557844103/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001557844103 none CCON(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H](C)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 5, 2, 1, 2, 1, 1, 1, 2, 2, 2, 6, 6, 6, 2, 2, 2, 5, 10, 10, 10, 19, 19, 18, 19, 19, 19, 6, 6, 6, 6, 6, 2, 6, 6, 2, 2, 2, 2, 10, 10, 10, 19, 19, 19, 19] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 84 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557844103 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001557844103 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557844103/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557844103/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557844103 Building ZINC001557844103 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557844103' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557844103 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001557844103 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557844103/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557844103 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 824) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCON(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H](C)c1cccc(Br)c1) `ZINC001557844103.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001557844103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557844103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001557844103 none CCON(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H](C)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 7, 7, 7, 2, 2, 2, 4, 5, 5, 5, 16, 16, 12, 16, 16, 16, 6, 6, 6, 6, 6, 2, 7, 7, 2, 2, 2, 2, 5, 5, 5, 16, 16, 12, 16] 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557844103 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557844103/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557844103 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 825) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCON(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H](C)c1cccc(Br)c1) `ZINC001557844103.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001557844103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557844103/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001557844103 none CCON(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H](C)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 5, 2, 1, 2, 1, 1, 1, 2, 2, 2, 6, 6, 6, 2, 2, 2, 5, 10, 10, 10, 19, 19, 18, 19, 19, 19, 6, 6, 6, 6, 6, 2, 6, 6, 2, 2, 2, 2, 10, 10, 10, 19, 19, 19, 19] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 84 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557844103 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001557844103 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557844103/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557844103/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557844103 Building ZINC001557844105 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557844105' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557844105 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001557844105 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557844105/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557844105 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 826) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/826 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/826' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCON(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@@H](C)c1cccc(Br)c1) `ZINC001557844105.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001557844105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557844105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001557844105 none CCON(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@@H](C)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 5, 2, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 5, 10, 10, 10, 18, 18, 18, 18, 18, 18, 6, 6, 6, 6, 6, 2, 5, 5, 2, 2, 2, 2, 10, 10, 10, 18, 18, 18, 18] 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]) total number of confs: 71 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557844105 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557844105/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557844105 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 827) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/827 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/827' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCON(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@@H](C)c1cccc(Br)c1) `ZINC001557844105.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001557844105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557844105/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001557844105 none CCON(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@@H](C)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 7, 7, 7, 2, 2, 2, 4, 6, 6, 6, 16, 16, 12, 16, 16, 16, 5, 5, 5, 5, 5, 2, 7, 7, 2, 2, 2, 2, 6, 6, 6, 16, 16, 16, 16] 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]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557844105 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001557844105 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557844105/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557844105/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557844105 Building ZINC001557844105 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557844105' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557844105 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001557844105 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557844105/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557844105 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 826) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCON(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@@H](C)c1cccc(Br)c1) `ZINC001557844105.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001557844105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557844105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001557844105 none CCON(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@@H](C)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 5, 2, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 5, 10, 10, 10, 18, 18, 18, 18, 18, 18, 6, 6, 6, 6, 6, 2, 5, 5, 2, 2, 2, 2, 10, 10, 10, 18, 18, 18, 18] 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]) total number of confs: 71 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557844105 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557844105/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557844105 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 827) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCON(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@@H](C)c1cccc(Br)c1) `ZINC001557844105.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001557844105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557844105/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001557844105 none CCON(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@@H](C)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 7, 7, 7, 2, 2, 2, 4, 6, 6, 6, 16, 16, 12, 16, 16, 16, 5, 5, 5, 5, 5, 2, 7, 7, 2, 2, 2, 2, 6, 6, 6, 16, 16, 16, 16] 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]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557844105 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001557844105 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557844105/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557844105/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001557844105 Building ZINC001558306120 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558306120' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558306120 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001558306120 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558306120/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558306120 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 828) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/828 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/828' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](CC1CN(C(=O)OC(C)(C)C)C1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC001558306120.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001558306120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558306120/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 69 natoms 68 natoms 67 natoms 66 names: ZINC001558306120 none CCOC(=O)[C@H](CC1CN(C(=O)OC(C)(C)C)C1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 6, 6, 6, 2, 6, 6, 18, 35, 35, 35, 45, 45, 45, 45, 45, 45, 35, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 5, 5, 5, 4, 10, 10, 10, 10, 10, 11, 11, 35, 35, 35, 45, 45, 45, 45, 45, 45, 45, 45, 45, 35, 35, 2, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558306120 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558306120/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558306120 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 829) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/829 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/829' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](CC1CN(C(=O)OC(C)(C)C)C1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC001558306120.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001558306120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558306120/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 69 natoms 68 natoms 67 natoms 66 names: ZINC001558306120 none CCOC(=O)[C@H](CC1CN(C(=O)OC(C)(C)C)C1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 5, 5, 16, 30, 30, 30, 41, 41, 41, 41, 41, 41, 30, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 6, 6, 6, 5, 7, 7, 7, 7, 7, 10, 10, 30, 30, 30, 41, 41, 41, 41, 41, 41, 41, 41, 41, 30, 30, 2, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558306120 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001558306120 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558306120/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558306120/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558306120 Building ZINC001558306120 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558306120' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558306120 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001558306120 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558306120/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558306120 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 828) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/828: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](CC1CN(C(=O)OC(C)(C)C)C1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC001558306120.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001558306120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558306120/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 69 natoms 68 natoms 67 natoms 66 names: ZINC001558306120 none CCOC(=O)[C@H](CC1CN(C(=O)OC(C)(C)C)C1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 6, 6, 6, 2, 6, 6, 18, 35, 35, 35, 45, 45, 45, 45, 45, 45, 35, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 5, 5, 5, 4, 10, 10, 10, 10, 10, 11, 11, 35, 35, 35, 45, 45, 45, 45, 45, 45, 45, 45, 45, 35, 35, 2, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558306120 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558306120/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558306120 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 829) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/829: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](CC1CN(C(=O)OC(C)(C)C)C1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC001558306120.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001558306120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558306120/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 69 natoms 68 natoms 67 natoms 66 names: ZINC001558306120 none CCOC(=O)[C@H](CC1CN(C(=O)OC(C)(C)C)C1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 5, 5, 16, 30, 30, 30, 41, 41, 41, 41, 41, 41, 30, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 6, 6, 6, 5, 7, 7, 7, 7, 7, 10, 10, 30, 30, 30, 41, 41, 41, 41, 41, 41, 41, 41, 41, 30, 30, 2, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558306120 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001558306120 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558306120/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558306120/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558306120 Building ZINC001558306121 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558306121' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558306121 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001558306121 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558306121/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558306121 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 830) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/830 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/830' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](CC1CN(C(=O)OC(C)(C)C)C1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC001558306121.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001558306121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558306121/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 69 natoms 68 natoms 67 natoms 66 names: ZINC001558306121 none CCOC(=O)[C@@H](CC1CN(C(=O)OC(C)(C)C)C1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 2, 5, 5, 18, 32, 32, 32, 41, 41, 41, 41, 41, 41, 32, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 5, 8, 8, 8, 8, 8, 10, 10, 32, 32, 32, 41, 41, 41, 41, 41, 41, 41, 41, 41, 32, 32, 2, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558306121 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558306121/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558306121 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 831) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/831 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/831' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](CC1CN(C(=O)OC(C)(C)C)C1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC001558306121.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001558306121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558306121/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 69 natoms 68 natoms 67 natoms 66 names: ZINC001558306121 none CCOC(=O)[C@@H](CC1CN(C(=O)OC(C)(C)C)C1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 6, 6, 6, 2, 6, 6, 21, 34, 34, 34, 44, 44, 44, 44, 44, 44, 34, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 4, 10, 10, 10, 10, 10, 12, 12, 34, 34, 34, 44, 44, 44, 44, 44, 44, 44, 44, 44, 34, 34, 2, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558306121 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001558306121 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558306121/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558306121/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558306121 Building ZINC001558306121 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558306121' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558306121 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001558306121 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558306121/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558306121 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 830) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCOC(=O)[C@@H](CC1CN(C(=O)OC(C)(C)C)C1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC001558306121.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001558306121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558306121/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 69 natoms 68 natoms 67 natoms 66 names: ZINC001558306121 none CCOC(=O)[C@@H](CC1CN(C(=O)OC(C)(C)C)C1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 2, 5, 5, 18, 32, 32, 32, 41, 41, 41, 41, 41, 41, 32, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 5, 8, 8, 8, 8, 8, 10, 10, 32, 32, 32, 41, 41, 41, 41, 41, 41, 41, 41, 41, 32, 32, 2, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558306121 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558306121/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558306121 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 831) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCOC(=O)[C@@H](CC1CN(C(=O)OC(C)(C)C)C1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC001558306121.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001558306121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558306121/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 69 natoms 68 natoms 67 natoms 66 names: ZINC001558306121 none CCOC(=O)[C@@H](CC1CN(C(=O)OC(C)(C)C)C1)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 6, 6, 6, 2, 6, 6, 21, 34, 34, 34, 44, 44, 44, 44, 44, 44, 34, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 4, 10, 10, 10, 10, 10, 12, 12, 34, 34, 34, 44, 44, 44, 44, 44, 44, 44, 44, 44, 34, 34, 2, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558306121 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001558306121 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558306121/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558306121/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558306121 Building ZINC001558798935 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558798935' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558798935 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001558798935 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558798935/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558798935 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 832) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/832 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/832' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCN(C(=O)[C@@H](Cc2ccccc2)NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001558798935.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001558798935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558798935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001558798935 none CCN1CCN(C(=O)[C@@H](Cc2ccccc2)NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 11, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 33, 33, 33, 19, 6, 15, 4, 6, 6, 9, 9, 9, 9, 9, 9, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 33, 33, 35, 35, 35, 35, 35, 33, 33, 33, 33, 9, 9, 9, 9, 9, 9, 9, 4, 4, 4, 4, 4, 33, 33, 33, 33] 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, 58, 59]) total number of confs: 110 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558798935 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558798935/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558798935 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 833) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/833 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/833' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCN(C(=O)[C@@H](Cc2ccccc2)NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001558798935.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001558798935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558798935/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001558798935 none CCN1CCN(C(=O)[C@@H](Cc2ccccc2)NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 11, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 29, 29, 19, 7, 16, 4, 7, 7, 10, 10, 10, 10, 10, 10, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 29, 29, 31, 31, 31, 31, 31, 29, 29, 29, 29, 10, 10, 10, 10, 10, 10, 10, 4, 5, 5, 5, 5, 29, 29, 29, 29] 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, 58, 59]) total number of confs: 102 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558798935 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001558798935 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558798935/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558798935/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558798935 Building ZINC001558798935 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558798935' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558798935 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001558798935 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558798935/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558798935 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 832) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/832: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCN(C(=O)[C@@H](Cc2ccccc2)NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001558798935.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001558798935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558798935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001558798935 none CCN1CCN(C(=O)[C@@H](Cc2ccccc2)NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 11, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 33, 33, 33, 19, 6, 15, 4, 6, 6, 9, 9, 9, 9, 9, 9, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 33, 33, 35, 35, 35, 35, 35, 33, 33, 33, 33, 9, 9, 9, 9, 9, 9, 9, 4, 4, 4, 4, 4, 33, 33, 33, 33] 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, 58, 59]) total number of confs: 110 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558798935 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558798935/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558798935 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 833) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/833: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCN(C(=O)[C@@H](Cc2ccccc2)NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001558798935.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001558798935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558798935/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001558798935 none CCN1CCN(C(=O)[C@@H](Cc2ccccc2)NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 11, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 29, 29, 19, 7, 16, 4, 7, 7, 10, 10, 10, 10, 10, 10, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 29, 29, 31, 31, 31, 31, 31, 29, 29, 29, 29, 10, 10, 10, 10, 10, 10, 10, 4, 5, 5, 5, 5, 29, 29, 29, 29] 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, 58, 59]) total number of confs: 102 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558798935 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001558798935 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558798935/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558798935/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558798935 Building ZINC001558798936 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558798936' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558798936 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001558798936 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558798936/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558798936 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 834) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/834 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/834' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCN(C(=O)[C@H](Cc2ccccc2)NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001558798936.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001558798936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558798936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001558798936 none CCN1CCN(C(=O)[C@H](Cc2ccccc2)NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 11, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 24, 24, 24, 24, 16, 8, 15, 4, 8, 8, 13, 13, 13, 13, 13, 13, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 29, 29, 29, 29, 29, 24, 24, 24, 24, 13, 13, 13, 13, 13, 13, 13, 4, 6, 6, 6, 6, 24, 24, 24, 24] 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, 58, 59]) total number of confs: 130 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558798936 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558798936/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558798936 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 835) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/835 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/835' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCN(C(=O)[C@H](Cc2ccccc2)NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001558798936.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001558798936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558798936/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001558798936 none CCN1CCN(C(=O)[C@H](Cc2ccccc2)NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 11, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 27, 27, 16, 7, 15, 4, 7, 7, 11, 11, 11, 11, 11, 11, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 29, 29, 29, 29, 29, 27, 27, 27, 27, 11, 11, 11, 11, 11, 11, 11, 4, 6, 6, 6, 6, 27, 27, 27, 27] 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, 58, 59]) total number of confs: 109 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558798936 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001558798936 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558798936/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558798936/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558798936 Building ZINC001558798936 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558798936' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558798936 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001558798936 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558798936/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558798936 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 834) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCN1CCN(C(=O)[C@H](Cc2ccccc2)NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001558798936.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001558798936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558798936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001558798936 none CCN1CCN(C(=O)[C@H](Cc2ccccc2)NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 11, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 24, 24, 24, 24, 16, 8, 15, 4, 8, 8, 13, 13, 13, 13, 13, 13, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 29, 29, 29, 29, 29, 24, 24, 24, 24, 13, 13, 13, 13, 13, 13, 13, 4, 6, 6, 6, 6, 24, 24, 24, 24] 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, 58, 59]) total number of confs: 130 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558798936 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558798936/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558798936 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 835) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCN1CCN(C(=O)[C@H](Cc2ccccc2)NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001558798936.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001558798936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558798936/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001558798936 none CCN1CCN(C(=O)[C@H](Cc2ccccc2)NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 11, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 27, 27, 16, 7, 15, 4, 7, 7, 11, 11, 11, 11, 11, 11, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 29, 29, 29, 29, 29, 27, 27, 27, 27, 11, 11, 11, 11, 11, 11, 11, 4, 6, 6, 6, 6, 27, 27, 27, 27] 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, 58, 59]) total number of confs: 109 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558798936 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001558798936 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558798936/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558798936/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001558798936 Building ZINC001559042463 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001559042463' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001559042463 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001559042463 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001559042463/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001559042463 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 836) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/836 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/836' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CCO1) `ZINC001559042463.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001559042463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001559042463/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001559042463 none CCOC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 12, 12, 5, 12, 5, 5, 5, 4, 1, 5, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 5, 5, 5, 14, 14, 14, 14, 14, 5, 5, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 5, 5, 5, 5] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 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/418326/xbt-8058088.46/working/building/ZINC001559042463 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001559042463/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001559042463 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 837) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/837 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/837' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CCO1) `ZINC001559042463.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001559042463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001559042463/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001559042463 none CCOC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 3, 10, 3, 3, 3, 2, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 3, 3, 3, 13, 13, 13, 13, 13, 3, 3, 2, 2, 2, 10, 10, 10, 10, 2, 2, 2, 3, 3, 3, 3] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001559042463 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001559042463 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001559042463/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001559042463/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001559042463 Building ZINC001559042463 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001559042463' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001559042463 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001559042463 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001559042463/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001559042463 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 836) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCOC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CCO1) `ZINC001559042463.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001559042463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001559042463/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001559042463 none CCOC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 12, 12, 5, 12, 5, 5, 5, 4, 1, 5, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 5, 5, 5, 14, 14, 14, 14, 14, 5, 5, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 5, 5, 5, 5] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 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/418326/xbt-8058088.46/working/building/ZINC001559042463 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001559042463/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001559042463 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 837) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCOC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CCO1) `ZINC001559042463.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001559042463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001559042463/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001559042463 none CCOC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 3, 10, 3, 3, 3, 2, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 3, 3, 3, 13, 13, 13, 13, 13, 3, 3, 2, 2, 2, 10, 10, 10, 10, 2, 2, 2, 3, 3, 3, 3] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001559042463 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001559042463 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001559042463/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001559042463/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001559042463 Building ZINC001559042464 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001559042464' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001559042464 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001559042464 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001559042464/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001559042464 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 838) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/838 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/838' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CCO1) `ZINC001559042464.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001559042464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001559042464/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001559042464 none CCOC(=O)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 9, 4, 4, 4, 3, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 4, 4, 4, 9, 9, 9, 9, 9, 4, 4, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001559042464 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001559042464/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001559042464 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 839) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/839 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/839' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CCO1) `ZINC001559042464.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001559042464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001559042464/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001559042464 none CCOC(=O)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 5, 13, 5, 5, 5, 3, 1, 5, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 5, 5, 5, 13, 13, 13, 13, 13, 5, 5, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 5, 5, 5, 5] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001559042464 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001559042464 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001559042464/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001559042464/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001559042464 Building ZINC001559042464 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001559042464' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001559042464 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001559042464 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001559042464/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001559042464 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 838) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCOC(=O)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CCO1) `ZINC001559042464.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001559042464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001559042464/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001559042464 none CCOC(=O)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 9, 4, 4, 4, 3, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 4, 4, 4, 9, 9, 9, 9, 9, 4, 4, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001559042464 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001559042464/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001559042464 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 839) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCOC(=O)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CCO1) `ZINC001559042464.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001559042464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001559042464/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001559042464 none CCOC(=O)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 5, 13, 5, 5, 5, 3, 1, 5, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 5, 5, 5, 13, 13, 13, 13, 13, 5, 5, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 5, 5, 5, 5] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001559042464 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001559042464 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001559042464/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001559042464/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001559042464 Building ZINC001565615977 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565615977' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565615977 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001565615977 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565615977/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565615977 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 840) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/840 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/840' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)n1c2ccccc2nc1[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001565615977.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001565615977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565615977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001565615977 none CC(C)n1c2ccccc2nc1[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 9, 9, 9, 9, 9, 9, 6, 1, 6, 1, 1, 1, 3, 3, 3, 12, 12, 12, 3, 3, 3, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 9, 9, 9, 9, 9, 9, 3, 12, 12, 3, 3, 3, 3, 9, 9] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 66 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565615977 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565615977/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565615977 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 841) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/841 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/841' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)n1c2ccccc2nc1[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001565615977.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001565615977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565615977/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001565615977 none CC(C)n1c2ccccc2nc1[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 9, 9, 9, 9, 9, 6, 2, 7, 1, 1, 1, 5, 5, 5, 13, 13, 13, 5, 5, 5, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 9, 9, 9, 9, 9, 5, 13, 13, 5, 5, 5, 5, 9, 9] 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, 56, 57, 58]) total number of confs: 75 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565615977 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001565615977 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565615977/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565615977/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565615977 Building ZINC001565615977 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565615977' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565615977 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001565615977 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565615977/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565615977 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 840) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC(C)n1c2ccccc2nc1[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001565615977.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001565615977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565615977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001565615977 none CC(C)n1c2ccccc2nc1[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 9, 9, 9, 9, 9, 9, 6, 1, 6, 1, 1, 1, 3, 3, 3, 12, 12, 12, 3, 3, 3, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 9, 9, 9, 9, 9, 9, 3, 12, 12, 3, 3, 3, 3, 9, 9] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 66 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565615977 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565615977/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565615977 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 841) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC(C)n1c2ccccc2nc1[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001565615977.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001565615977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565615977/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001565615977 none CC(C)n1c2ccccc2nc1[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 9, 9, 9, 9, 9, 6, 2, 7, 1, 1, 1, 5, 5, 5, 13, 13, 13, 5, 5, 5, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 9, 9, 9, 9, 9, 5, 13, 13, 5, 5, 5, 5, 9, 9] 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, 56, 57, 58]) total number of confs: 75 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565615977 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001565615977 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565615977/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565615977/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565615977 Building ZINC001565615978 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565615978' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565615978 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001565615978 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565615978/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565615978 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 842) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/842 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/842' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)n1c2ccccc2nc1[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001565615978.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001565615978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565615978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001565615978 none CC(C)n1c2ccccc2nc1[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 9, 7, 2, 5, 1, 1, 1, 4, 4, 4, 12, 12, 12, 4, 4, 4, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 9, 9, 9, 9, 9, 9, 4, 12, 12, 4, 4, 4, 4, 9, 9] 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, 56, 57, 58]) total number of confs: 67 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565615978 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565615978/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565615978 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 843) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/843 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/843' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)n1c2ccccc2nc1[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001565615978.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001565615978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565615978/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001565615978 none CC(C)n1c2ccccc2nc1[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 8, 8, 8, 8, 8, 5, 2, 4, 1, 1, 1, 3, 3, 3, 12, 12, 12, 3, 3, 3, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 8, 8, 8, 8, 8, 3, 12, 12, 3, 3, 3, 3, 8, 8] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 66 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565615978 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001565615978 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565615978/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565615978/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565615978 Building ZINC001565615978 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565615978' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565615978 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001565615978 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565615978/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565615978 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 842) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC(C)n1c2ccccc2nc1[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001565615978.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001565615978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565615978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001565615978 none CC(C)n1c2ccccc2nc1[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 9, 7, 2, 5, 1, 1, 1, 4, 4, 4, 12, 12, 12, 4, 4, 4, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 9, 9, 9, 9, 9, 9, 4, 12, 12, 4, 4, 4, 4, 9, 9] 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, 56, 57, 58]) total number of confs: 67 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565615978 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565615978/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565615978 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 843) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC(C)n1c2ccccc2nc1[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001565615978.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001565615978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565615978/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001565615978 none CC(C)n1c2ccccc2nc1[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['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', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 8, 8, 8, 8, 8, 5, 2, 4, 1, 1, 1, 3, 3, 3, 12, 12, 12, 3, 3, 3, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 8, 8, 8, 8, 8, 3, 12, 12, 3, 3, 3, 3, 8, 8] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 66 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565615978 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001565615978 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565615978/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565615978/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565615978 Building ZINC001565640652 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565640652' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565640652 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001565640652 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565640652/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565640652 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 844) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/844 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/844' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](NS(=O)(=O)c2cccc(F)c2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001565640652.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001565640652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565640652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001565640652 none O=C(N1CCC[C@@H](NS(=O)(=O)c2cccc(F)c2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 8, 14, 11, 11, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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] 0 hydrogens need 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, 4, 4, 4, 4, 4, 4, 4, 9, 17, 17, 17, 29, 29, 29, 29, 29, 29, 4, 1, 1, 1, 4, 4, 4, 4, 6, 6, 4, 6, 6, 4, 4, 4, 4, 4, 4, 4, 9, 29, 29, 29, 29, 4, 4, 4, 6, 6, 4, 6, 6, 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]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565640652 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565640652/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565640652 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 845) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/845 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/845' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](NS(=O)(=O)c2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001565640652.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001565640652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565640652/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001565640652 none O=C(N1CCC[C@@H](NS(=O)(=O)c2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 8, 14, 11, 11, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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] 0 hydrogens need 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, 9, 9, 9, 9, 9, 9, 17, 23, 23, 23, 38, 38, 38, 38, 38, 38, 9, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 17, 38, 38, 38, 38, 9, 9, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 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/418326/xbt-8058088.46/working/building/ZINC001565640652 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001565640652 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565640652/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565640652/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565640652 Building ZINC001565640652 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565640652' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565640652 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001565640652 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565640652/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565640652 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 844) grep: /scratch/xiaobo/418326/xbt-8058088.46/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(N1CCC[C@@H](NS(=O)(=O)c2cccc(F)c2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001565640652.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001565640652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565640652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001565640652 none O=C(N1CCC[C@@H](NS(=O)(=O)c2cccc(F)c2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 8, 14, 11, 11, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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] 0 hydrogens need 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, 4, 4, 4, 4, 4, 4, 4, 9, 17, 17, 17, 29, 29, 29, 29, 29, 29, 4, 1, 1, 1, 4, 4, 4, 4, 6, 6, 4, 6, 6, 4, 4, 4, 4, 4, 4, 4, 9, 29, 29, 29, 29, 4, 4, 4, 6, 6, 4, 6, 6, 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]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565640652 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565640652/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565640652 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 845) grep: /scratch/xiaobo/418326/xbt-8058088.46/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(N1CCC[C@@H](NS(=O)(=O)c2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001565640652.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001565640652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565640652/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001565640652 none O=C(N1CCC[C@@H](NS(=O)(=O)c2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 8, 14, 11, 11, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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] 0 hydrogens need 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, 9, 9, 9, 9, 9, 9, 17, 23, 23, 23, 38, 38, 38, 38, 38, 38, 9, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 17, 38, 38, 38, 38, 9, 9, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 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/418326/xbt-8058088.46/working/building/ZINC001565640652 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001565640652 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565640652/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565640652/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565640652 Building ZINC001565640653 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565640653' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565640653 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001565640653 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565640653/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565640653 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 846) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/846 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/846' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H](NS(=O)(=O)c2cccc(F)c2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001565640653.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001565640653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565640653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001565640653 none O=C(N1CCC[C@H](NS(=O)(=O)c2cccc(F)c2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 8, 14, 11, 11, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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] 0 hydrogens need 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, 9, 9, 9, 9, 9, 9, 16, 24, 24, 24, 39, 39, 39, 39, 39, 39, 9, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 16, 39, 39, 39, 39, 9, 9, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565640653 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565640653/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565640653 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 847) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/847 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/847' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H](NS(=O)(=O)c2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001565640653.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001565640653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565640653/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001565640653 none O=C(N1CCC[C@H](NS(=O)(=O)c2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 8, 14, 11, 11, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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] 0 hydrogens need 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, 4, 5, 5, 5, 5, 5, 5, 10, 18, 18, 18, 31, 31, 31, 31, 31, 31, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 10, 31, 31, 31, 31, 5, 5, 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565640653 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001565640653 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565640653/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565640653/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565640653 Building ZINC001565640653 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565640653' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565640653 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001565640653 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565640653/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565640653 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 846) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/846: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H](NS(=O)(=O)c2cccc(F)c2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001565640653.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001565640653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565640653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001565640653 none O=C(N1CCC[C@H](NS(=O)(=O)c2cccc(F)c2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 8, 14, 11, 11, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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] 0 hydrogens need 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, 9, 9, 9, 9, 9, 9, 16, 24, 24, 24, 39, 39, 39, 39, 39, 39, 9, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 16, 39, 39, 39, 39, 9, 9, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565640653 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565640653/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565640653 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 847) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/847: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H](NS(=O)(=O)c2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001565640653.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001565640653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565640653/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001565640653 none O=C(N1CCC[C@H](NS(=O)(=O)c2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 8, 14, 11, 11, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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] 0 hydrogens need 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, 4, 5, 5, 5, 5, 5, 5, 10, 18, 18, 18, 31, 31, 31, 31, 31, 31, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 10, 31, 31, 31, 31, 5, 5, 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565640653 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001565640653 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565640653/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565640653/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565640653 Building ZINC001565655027 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565655027' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565655027 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001565655027 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565655027/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565655027 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 848) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/848 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/848' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1ccccc1)c1ccc2c(c1)CCCO2) `ZINC001565655027.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001565655027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565655027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001565655027 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1ccccc1)c1ccc2c(c1)CCCO2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', '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.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 8, 8, 4, 8, 8, 4, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 4, 4, 1, 2, 8, 8, 4, 8, 8, 19, 19, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [0, 1, 34, 35, 36, 33, 8, 9, 10, 39, 12, 2, 11, 3, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 62 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565655027 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565655027/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565655027 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 849) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/849 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/849' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H](c1ccccc1)c1ccc2c(c1)CCCO2) `ZINC001565655027.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001565655027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565655027/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001565655027 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H](c1ccccc1)c1ccc2c(c1)CCCO2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', '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.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 3, 1, 1, 1, 1, 3, 3, 3, 6, 6, 9, 9, 7, 9, 9, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 3, 3, 3, 3, 7, 7, 3, 3, 9, 9, 7, 9, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 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: 74 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565655027 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001565655027 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565655027/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565655027/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565655027 Building ZINC001565655027 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565655027' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565655027 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001565655027 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565655027/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565655027 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 848) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1ccccc1)c1ccc2c(c1)CCCO2) `ZINC001565655027.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001565655027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565655027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001565655027 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1ccccc1)c1ccc2c(c1)CCCO2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', '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.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 8, 8, 4, 8, 8, 4, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 4, 4, 1, 2, 8, 8, 4, 8, 8, 19, 19, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [0, 1, 34, 35, 36, 33, 8, 9, 10, 39, 12, 2, 11, 3, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 62 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565655027 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565655027/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565655027 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 849) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H](c1ccccc1)c1ccc2c(c1)CCCO2) `ZINC001565655027.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001565655027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565655027/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001565655027 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H](c1ccccc1)c1ccc2c(c1)CCCO2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', '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.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 3, 1, 1, 1, 1, 3, 3, 3, 6, 6, 9, 9, 7, 9, 9, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 3, 3, 3, 3, 7, 7, 3, 3, 9, 9, 7, 9, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 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: 74 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565655027 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001565655027 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565655027/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565655027/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565655027 Building ZINC001565655028 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565655028' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565655028 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001565655028 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565655028/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565655028 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 850) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/850 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/850' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H](c1ccccc1)c1ccc2c(c1)CCCO2) `ZINC001565655028.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001565655028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565655028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001565655028 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H](c1ccccc1)c1ccc2c(c1)CCCO2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', '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.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 5, 2, 1, 1, 1, 1, 3, 3, 3, 6, 6, 9, 9, 6, 9, 9, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 2, 2, 2, 2, 5, 5, 2, 3, 9, 9, 6, 9, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 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: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565655028 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565655028/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565655028 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 851) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/851 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/851' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H](c1ccccc1)c1ccc2c(c1)CCCO2) `ZINC001565655028.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001565655028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565655028/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001565655028 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H](c1ccccc1)c1ccc2c(c1)CCCO2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', '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.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 8, 8, 4, 8, 8, 4, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 4, 4, 1, 2, 8, 8, 4, 8, 8, 19, 19, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [0, 1, 34, 35, 36, 33, 8, 9, 10, 39, 12, 2, 11, 3, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 62 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565655028 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001565655028 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565655028/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565655028/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565655028 Building ZINC001565655028 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565655028' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565655028 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001565655028 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565655028/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565655028 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 850) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/850: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H](c1ccccc1)c1ccc2c(c1)CCCO2) `ZINC001565655028.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001565655028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565655028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001565655028 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H](c1ccccc1)c1ccc2c(c1)CCCO2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', '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.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 5, 2, 1, 1, 1, 1, 3, 3, 3, 6, 6, 9, 9, 6, 9, 9, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 2, 2, 2, 2, 5, 5, 2, 3, 9, 9, 6, 9, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 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: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565655028 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565655028/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565655028 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 851) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/851: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H](c1ccccc1)c1ccc2c(c1)CCCO2) `ZINC001565655028.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001565655028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565655028/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001565655028 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H](c1ccccc1)c1ccc2c(c1)CCCO2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', '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.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 8, 8, 4, 8, 8, 4, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 4, 4, 1, 2, 8, 8, 4, 8, 8, 19, 19, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [0, 1, 34, 35, 36, 33, 8, 9, 10, 39, 12, 2, 11, 3, 4] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 62 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565655028 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001565655028 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565655028/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565655028/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565655028 Building ZINC001565696224 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565696224' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565696224 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001565696224 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565696224/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565696224 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 852) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/852 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/852' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCc1ccc(Oc2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)cc2)cc1) `ZINC001565696224.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001565696224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565696224/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001565696224 none COCCc1ccc(Oc2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', '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.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 34, 34, 18, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 8, 8, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 8, 8, 2, 1, 3, 3, 1, 1, 1, 1, 8, 8, 34, 34] 50 rigid atoms, others: [48, 49, 44, 50, 14, 47, 16, 17, 18, 19, 20, 21, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 51, 52, 53, 54]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565696224 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565696224/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565696224 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 853) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/853 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/853' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCc1ccc(Oc2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)cc2)cc1) `ZINC001565696224.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001565696224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565696224/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001565696224 none COCCc1ccc(Oc2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', '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.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 33, 33, 17, 2, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 8, 8, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 8, 8, 2, 1, 3, 3, 1, 1, 1, 1, 8, 8, 33, 33] 50 rigid atoms, others: [48, 49, 44, 50, 14, 47, 16, 17, 18, 19, 20, 21, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 51, 52, 53, 54]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565696224 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001565696224 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565696224/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565696224/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565696224 Building ZINC001565696224 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565696224' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565696224 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001565696224 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565696224/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565696224 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 852) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COCCc1ccc(Oc2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)cc2)cc1) `ZINC001565696224.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001565696224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565696224/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001565696224 none COCCc1ccc(Oc2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', '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.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 34, 34, 18, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 8, 8, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 8, 8, 2, 1, 3, 3, 1, 1, 1, 1, 8, 8, 34, 34] 50 rigid atoms, others: [48, 49, 44, 50, 14, 47, 16, 17, 18, 19, 20, 21, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 51, 52, 53, 54]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565696224 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565696224/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565696224 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 853) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COCCc1ccc(Oc2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)cc2)cc1) `ZINC001565696224.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001565696224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565696224/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001565696224 none COCCc1ccc(Oc2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', '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.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 33, 33, 17, 2, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 8, 8, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 8, 8, 2, 1, 3, 3, 1, 1, 1, 1, 8, 8, 33, 33] 50 rigid atoms, others: [48, 49, 44, 50, 14, 47, 16, 17, 18, 19, 20, 21, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 51, 52, 53, 54]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565696224 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001565696224 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565696224/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565696224/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565696224 Building ZINC001565711654 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001565711654 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 854) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/854 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/854' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)S(=O)(=O)c1ccc([N@]2CC[N@](C)CC2)c(NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)c1) `ZINC001565711654.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001565711654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001565711654 none CCN(CC)S(=O)(=O)c1ccc([N@]2CC[N@](C)CC2)c(NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 14, 11, 11, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 17, 18, 4, 12, 12, 4, 4, 4, 4, 5, 10, 10, 10, 10, 10, 10, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 4, 17, 17, 17, 17, 17, 18, 18, 18, 18, 18, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 855) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/855 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/855' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)S(=O)(=O)c1ccc([N@]2CC[N@](C)CC2)c(NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)c1) `ZINC001565711654.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001565711654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001565711654 none CCN(CC)S(=O)(=O)c1ccc([N@]2CC[N@](C)CC2)c(NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 14, 11, 11, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 20, 14, 20, 20, 4, 14, 14, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 11, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 4, 21, 21, 21, 21, 21, 20, 20, 20, 20, 20, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 856) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/856 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/856' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)S(=O)(=O)c1ccc([N@]2CC[N@@](C)CC2)c(NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)c1) `ZINC001565711654.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001565711654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001565711654 none CCN(CC)S(=O)(=O)c1ccc([N@]2CC[N@@](C)CC2)c(NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 14, 11, 11, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 20, 21, 4, 14, 14, 4, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 4, 20, 20, 20, 20, 20, 21, 21, 21, 21, 21, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 857) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/857 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/857' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)S(=O)(=O)c1ccc([N@]2CC[N@@](C)CC2)c(NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)c1) `ZINC001565711654.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001565711654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001565711654 none CCN(CC)S(=O)(=O)c1ccc([N@]2CC[N@@](C)CC2)c(NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 14, 11, 11, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 19, 13, 19, 19, 4, 13, 13, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 11, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 4, 20, 20, 20, 20, 20, 19, 19, 19, 19, 19, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001565711654 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654 Building ZINC001565711654 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001565711654 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 854) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCN(CC)S(=O)(=O)c1ccc([N@]2CC[N@](C)CC2)c(NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)c1) `ZINC001565711654.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001565711654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001565711654 none CCN(CC)S(=O)(=O)c1ccc([N@]2CC[N@](C)CC2)c(NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 14, 11, 11, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 17, 18, 4, 12, 12, 4, 4, 4, 4, 5, 10, 10, 10, 10, 10, 10, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 4, 17, 17, 17, 17, 17, 18, 18, 18, 18, 18, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 855) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCN(CC)S(=O)(=O)c1ccc([N@]2CC[N@](C)CC2)c(NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)c1) `ZINC001565711654.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001565711654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001565711654 none CCN(CC)S(=O)(=O)c1ccc([N@]2CC[N@](C)CC2)c(NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 14, 11, 11, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 20, 14, 20, 20, 4, 14, 14, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 11, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 4, 21, 21, 21, 21, 21, 20, 20, 20, 20, 20, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 856) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/856: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)S(=O)(=O)c1ccc([N@]2CC[N@@](C)CC2)c(NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)c1) `ZINC001565711654.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001565711654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001565711654 none CCN(CC)S(=O)(=O)c1ccc([N@]2CC[N@@](C)CC2)c(NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 14, 11, 11, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 20, 21, 4, 14, 14, 4, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 4, 20, 20, 20, 20, 20, 21, 21, 21, 21, 21, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 857) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/857: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)S(=O)(=O)c1ccc([N@]2CC[N@@](C)CC2)c(NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)c1) `ZINC001565711654.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001565711654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001565711654 none CCN(CC)S(=O)(=O)c1ccc([N@]2CC[N@@](C)CC2)c(NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 14, 11, 11, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 19, 13, 19, 19, 4, 13, 13, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 11, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 4, 20, 20, 20, 20, 20, 19, 19, 19, 19, 19, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001565711654 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654 Building ZINC001565711654 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001565711654 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 854) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCN(CC)S(=O)(=O)c1ccc([N@]2CC[N@](C)CC2)c(NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)c1) `ZINC001565711654.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001565711654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001565711654 none CCN(CC)S(=O)(=O)c1ccc([N@]2CC[N@](C)CC2)c(NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 14, 11, 11, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 17, 18, 4, 12, 12, 4, 4, 4, 4, 5, 10, 10, 10, 10, 10, 10, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 4, 17, 17, 17, 17, 17, 18, 18, 18, 18, 18, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 855) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCN(CC)S(=O)(=O)c1ccc([N@]2CC[N@](C)CC2)c(NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)c1) `ZINC001565711654.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001565711654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001565711654 none CCN(CC)S(=O)(=O)c1ccc([N@]2CC[N@](C)CC2)c(NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 14, 11, 11, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 20, 14, 20, 20, 4, 14, 14, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 11, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 4, 21, 21, 21, 21, 21, 20, 20, 20, 20, 20, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 856) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/856: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)S(=O)(=O)c1ccc([N@]2CC[N@@](C)CC2)c(NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)c1) `ZINC001565711654.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001565711654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001565711654 none CCN(CC)S(=O)(=O)c1ccc([N@]2CC[N@@](C)CC2)c(NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 14, 11, 11, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 20, 21, 4, 14, 14, 4, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 4, 20, 20, 20, 20, 20, 21, 21, 21, 21, 21, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 857) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/857: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)S(=O)(=O)c1ccc([N@]2CC[N@@](C)CC2)c(NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)c1) `ZINC001565711654.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001565711654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001565711654 none CCN(CC)S(=O)(=O)c1ccc([N@]2CC[N@@](C)CC2)c(NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 14, 11, 11, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 19, 13, 19, 19, 4, 13, 13, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 11, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 4, 20, 20, 20, 20, 20, 19, 19, 19, 19, 19, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001565711654 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654 Building ZINC001565711654 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001565711654 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 854) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCN(CC)S(=O)(=O)c1ccc([N@]2CC[N@](C)CC2)c(NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)c1) `ZINC001565711654.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001565711654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001565711654 none CCN(CC)S(=O)(=O)c1ccc([N@]2CC[N@](C)CC2)c(NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 14, 11, 11, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 17, 18, 4, 12, 12, 4, 4, 4, 4, 5, 10, 10, 10, 10, 10, 10, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 4, 17, 17, 17, 17, 17, 18, 18, 18, 18, 18, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 855) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCN(CC)S(=O)(=O)c1ccc([N@]2CC[N@](C)CC2)c(NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)c1) `ZINC001565711654.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001565711654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001565711654 none CCN(CC)S(=O)(=O)c1ccc([N@]2CC[N@](C)CC2)c(NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 14, 11, 11, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 20, 14, 20, 20, 4, 14, 14, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 11, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 4, 21, 21, 21, 21, 21, 20, 20, 20, 20, 20, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 856) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/856: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)S(=O)(=O)c1ccc([N@]2CC[N@@](C)CC2)c(NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)c1) `ZINC001565711654.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001565711654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001565711654 none CCN(CC)S(=O)(=O)c1ccc([N@]2CC[N@@](C)CC2)c(NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 14, 11, 11, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 20, 21, 4, 14, 14, 4, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 4, 20, 20, 20, 20, 20, 21, 21, 21, 21, 21, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 857) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/857: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)S(=O)(=O)c1ccc([N@]2CC[N@@](C)CC2)c(NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)c1) `ZINC001565711654.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001565711654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001565711654 none CCN(CC)S(=O)(=O)c1ccc([N@]2CC[N@@](C)CC2)c(NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 14, 11, 11, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 19, 13, 19, 19, 4, 13, 13, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 11, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 4, 20, 20, 20, 20, 20, 19, 19, 19, 19, 19, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001565711654 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001565711654 Building ZINC001566274906 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001566274906 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 858) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/858 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/858' -> `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)N1CCN(C)C[C@@H]1CNC(=O)OC(C)(C)C) `ZINC001566274906.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001566274906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001566274906 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1CNC(=O)OC(C)(C)C NO_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', 'N.3', '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', '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, 10, 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, 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, 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] 0 hydrogens need rotated 50 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, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 23, 33, 33, 49, 49, 49, 49, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 23, 49, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 150 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 859) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/859 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/859' -> `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)N1CCN(C)C[C@@H]1CNC(=O)OC(C)(C)C) `ZINC001566274906.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001566274906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001566274906 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1CNC(=O)OC(C)(C)C NO_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', 'N.3', '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', '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, 10, 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, 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, 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] 0 hydrogens need rotated 50 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, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 16, 22, 22, 30, 30, 30, 30, 2, 2, 2, 6, 6, 2, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 16, 30, 30, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 109 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 860) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/860 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/860' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1CNC(=O)OC(C)(C)C) `ZINC001566274906.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001566274906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001566274906 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1CNC(=O)OC(C)(C)C NO_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', 'N.3', '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', '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, 10, 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, 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, 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] 0 hydrogens need rotated 50 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, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 23, 33, 33, 49, 49, 49, 49, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 23, 49, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 150 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 861) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/861 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/861' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1CNC(=O)OC(C)(C)C) `ZINC001566274906.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001566274906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001566274906 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1CNC(=O)OC(C)(C)C NO_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', 'N.3', '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', '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, 10, 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, 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, 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] 0 hydrogens need rotated 50 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, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 16, 22, 22, 30, 30, 30, 30, 2, 2, 2, 6, 6, 2, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 16, 30, 30, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 109 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001566274906 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906 Building ZINC001566274906 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001566274906 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 858) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1CNC(=O)OC(C)(C)C) `ZINC001566274906.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001566274906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001566274906 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1CNC(=O)OC(C)(C)C NO_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', 'N.3', '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', '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, 10, 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, 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, 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] 0 hydrogens need rotated 50 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, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 23, 33, 33, 49, 49, 49, 49, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 23, 49, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 150 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 859) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1CNC(=O)OC(C)(C)C) `ZINC001566274906.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001566274906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001566274906 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1CNC(=O)OC(C)(C)C NO_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', 'N.3', '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', '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, 10, 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, 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, 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] 0 hydrogens need rotated 50 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, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 16, 22, 22, 30, 30, 30, 30, 2, 2, 2, 6, 6, 2, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 16, 30, 30, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 109 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 860) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/860: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)N1CCN(C)C[C@@H]1CNC(=O)OC(C)(C)C) `ZINC001566274906.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001566274906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001566274906 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1CNC(=O)OC(C)(C)C NO_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', 'N.3', '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', '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, 10, 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, 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, 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] 0 hydrogens need rotated 50 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, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 23, 33, 33, 49, 49, 49, 49, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 23, 49, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 150 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 861) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/861: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)N1CCN(C)C[C@@H]1CNC(=O)OC(C)(C)C) `ZINC001566274906.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001566274906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001566274906 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1CNC(=O)OC(C)(C)C NO_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', 'N.3', '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', '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, 10, 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, 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, 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] 0 hydrogens need rotated 50 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, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 16, 22, 22, 30, 30, 30, 30, 2, 2, 2, 6, 6, 2, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 16, 30, 30, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 109 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001566274906 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906 Building ZINC001566274906 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001566274906 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 858) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1CNC(=O)OC(C)(C)C) `ZINC001566274906.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001566274906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001566274906 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1CNC(=O)OC(C)(C)C NO_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', 'N.3', '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', '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, 10, 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, 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, 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] 0 hydrogens need rotated 50 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, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 23, 33, 33, 49, 49, 49, 49, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 23, 49, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 150 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 859) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1CNC(=O)OC(C)(C)C) `ZINC001566274906.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001566274906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001566274906 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1CNC(=O)OC(C)(C)C NO_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', 'N.3', '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', '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, 10, 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, 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, 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] 0 hydrogens need rotated 50 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, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 16, 22, 22, 30, 30, 30, 30, 2, 2, 2, 6, 6, 2, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 16, 30, 30, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 109 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 860) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/860: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)N1CCN(C)C[C@@H]1CNC(=O)OC(C)(C)C) `ZINC001566274906.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001566274906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001566274906 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1CNC(=O)OC(C)(C)C NO_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', 'N.3', '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', '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, 10, 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, 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, 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] 0 hydrogens need rotated 50 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, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 23, 33, 33, 49, 49, 49, 49, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 23, 49, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 150 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 861) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/861: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)N1CCN(C)C[C@@H]1CNC(=O)OC(C)(C)C) `ZINC001566274906.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001566274906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001566274906 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1CNC(=O)OC(C)(C)C NO_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', 'N.3', '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', '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, 10, 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, 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, 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] 0 hydrogens need rotated 50 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, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 16, 22, 22, 30, 30, 30, 30, 2, 2, 2, 6, 6, 2, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 16, 30, 30, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 109 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001566274906 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906 Building ZINC001566274906 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001566274906 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 858) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1CNC(=O)OC(C)(C)C) `ZINC001566274906.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001566274906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001566274906 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1CNC(=O)OC(C)(C)C NO_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', 'N.3', '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', '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, 10, 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, 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, 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] 0 hydrogens need rotated 50 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, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 23, 33, 33, 49, 49, 49, 49, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 23, 49, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 150 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 859) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1CNC(=O)OC(C)(C)C) `ZINC001566274906.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001566274906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001566274906 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1CNC(=O)OC(C)(C)C NO_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', 'N.3', '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', '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, 10, 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, 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, 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] 0 hydrogens need rotated 50 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, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 16, 22, 22, 30, 30, 30, 30, 2, 2, 2, 6, 6, 2, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 16, 30, 30, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 109 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 860) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/860: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)N1CCN(C)C[C@@H]1CNC(=O)OC(C)(C)C) `ZINC001566274906.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001566274906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001566274906 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1CNC(=O)OC(C)(C)C NO_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', 'N.3', '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', '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, 10, 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, 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, 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] 0 hydrogens need rotated 50 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, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 23, 33, 33, 49, 49, 49, 49, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 23, 49, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 150 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 861) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/861: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)N1CCN(C)C[C@@H]1CNC(=O)OC(C)(C)C) `ZINC001566274906.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001566274906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001566274906 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1CNC(=O)OC(C)(C)C NO_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', 'N.3', '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', '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, 10, 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, 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, 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] 0 hydrogens need rotated 50 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, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 16, 22, 22, 30, 30, 30, 30, 2, 2, 2, 6, 6, 2, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 16, 30, 30, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 109 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001566274906 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274906 Building ZINC001566274907 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001566274907 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 862) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/862 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/862' -> `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)N1CCN(C)C[C@H]1CNC(=O)OC(C)(C)C) `ZINC001566274907.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001566274907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001566274907 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1CNC(=O)OC(C)(C)C NO_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', 'N.3', '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', '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, 10, 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, 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, 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] 0 hydrogens need rotated 50 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, 4, 6, 6, 2, 2, 1, 1, 1, 2, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 23, 30, 30, 34, 34, 34, 34, 2, 2, 2, 6, 6, 6, 6, 6, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 15, 23, 34, 34, 34, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 138 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 863) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/863 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/863' -> `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)N1CCN(C)C[C@H]1CNC(=O)OC(C)(C)C) `ZINC001566274907.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001566274907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001566274907 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1CNC(=O)OC(C)(C)C NO_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', 'N.3', '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', '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, 10, 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, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 1, 1, 1, 2, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 30, 42, 42, 44, 44, 44, 44, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 30, 44, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 156 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 864) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/864 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/864' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1CNC(=O)OC(C)(C)C) `ZINC001566274907.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001566274907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001566274907 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1CNC(=O)OC(C)(C)C NO_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', 'N.3', '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', '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, 10, 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, 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, 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] 0 hydrogens need rotated 50 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, 4, 6, 6, 2, 2, 1, 1, 1, 2, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 23, 30, 30, 34, 34, 34, 34, 2, 2, 2, 6, 6, 6, 6, 6, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 15, 23, 34, 34, 34, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 138 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 865) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/865 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/865' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1CNC(=O)OC(C)(C)C) `ZINC001566274907.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001566274907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001566274907 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1CNC(=O)OC(C)(C)C NO_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', 'N.3', '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', '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, 10, 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, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 1, 1, 1, 2, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 30, 42, 42, 44, 44, 44, 44, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 30, 44, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 156 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001566274907 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907 Building ZINC001566274907 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001566274907 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 862) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1CNC(=O)OC(C)(C)C) `ZINC001566274907.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001566274907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001566274907 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1CNC(=O)OC(C)(C)C NO_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', 'N.3', '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', '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, 10, 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, 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, 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] 0 hydrogens need rotated 50 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, 4, 6, 6, 2, 2, 1, 1, 1, 2, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 23, 30, 30, 34, 34, 34, 34, 2, 2, 2, 6, 6, 6, 6, 6, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 15, 23, 34, 34, 34, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 138 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 863) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1CNC(=O)OC(C)(C)C) `ZINC001566274907.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001566274907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001566274907 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1CNC(=O)OC(C)(C)C NO_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', 'N.3', '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', '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, 10, 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, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 1, 1, 1, 2, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 30, 42, 42, 44, 44, 44, 44, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 30, 44, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 156 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 864) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/864: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)N1CCN(C)C[C@H]1CNC(=O)OC(C)(C)C) `ZINC001566274907.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001566274907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001566274907 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1CNC(=O)OC(C)(C)C NO_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', 'N.3', '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', '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, 10, 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, 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, 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] 0 hydrogens need rotated 50 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, 4, 6, 6, 2, 2, 1, 1, 1, 2, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 23, 30, 30, 34, 34, 34, 34, 2, 2, 2, 6, 6, 6, 6, 6, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 15, 23, 34, 34, 34, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 138 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 865) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/865: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)N1CCN(C)C[C@H]1CNC(=O)OC(C)(C)C) `ZINC001566274907.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001566274907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001566274907 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1CNC(=O)OC(C)(C)C NO_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', 'N.3', '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', '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, 10, 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, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 1, 1, 1, 2, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 30, 42, 42, 44, 44, 44, 44, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 30, 44, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 156 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001566274907 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907 Building ZINC001566274907 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001566274907 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 862) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1CNC(=O)OC(C)(C)C) `ZINC001566274907.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001566274907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001566274907 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1CNC(=O)OC(C)(C)C NO_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', 'N.3', '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', '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, 10, 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, 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, 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] 0 hydrogens need rotated 50 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, 4, 6, 6, 2, 2, 1, 1, 1, 2, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 23, 30, 30, 34, 34, 34, 34, 2, 2, 2, 6, 6, 6, 6, 6, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 15, 23, 34, 34, 34, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 138 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 863) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1CNC(=O)OC(C)(C)C) `ZINC001566274907.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001566274907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001566274907 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1CNC(=O)OC(C)(C)C NO_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', 'N.3', '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', '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, 10, 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, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 1, 1, 1, 2, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 30, 42, 42, 44, 44, 44, 44, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 30, 44, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 156 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 864) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/864: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)N1CCN(C)C[C@H]1CNC(=O)OC(C)(C)C) `ZINC001566274907.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001566274907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001566274907 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1CNC(=O)OC(C)(C)C NO_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', 'N.3', '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', '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, 10, 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, 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, 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] 0 hydrogens need rotated 50 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, 4, 6, 6, 2, 2, 1, 1, 1, 2, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 23, 30, 30, 34, 34, 34, 34, 2, 2, 2, 6, 6, 6, 6, 6, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 15, 23, 34, 34, 34, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 138 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 865) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/865: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)N1CCN(C)C[C@H]1CNC(=O)OC(C)(C)C) `ZINC001566274907.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001566274907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001566274907 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1CNC(=O)OC(C)(C)C NO_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', 'N.3', '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', '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, 10, 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, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 1, 1, 1, 2, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 30, 42, 42, 44, 44, 44, 44, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 30, 44, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 156 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001566274907 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907 Building ZINC001566274907 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001566274907 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 862) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1CNC(=O)OC(C)(C)C) `ZINC001566274907.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001566274907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001566274907 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1CNC(=O)OC(C)(C)C NO_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', 'N.3', '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', '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, 10, 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, 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, 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] 0 hydrogens need rotated 50 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, 4, 6, 6, 2, 2, 1, 1, 1, 2, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 23, 30, 30, 34, 34, 34, 34, 2, 2, 2, 6, 6, 6, 6, 6, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 15, 23, 34, 34, 34, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 138 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 863) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1CNC(=O)OC(C)(C)C) `ZINC001566274907.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001566274907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001566274907 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1CNC(=O)OC(C)(C)C NO_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', 'N.3', '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', '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, 10, 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, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 1, 1, 1, 2, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 30, 42, 42, 44, 44, 44, 44, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 30, 44, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 156 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 864) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/864: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)N1CCN(C)C[C@H]1CNC(=O)OC(C)(C)C) `ZINC001566274907.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001566274907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001566274907 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1CNC(=O)OC(C)(C)C NO_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', 'N.3', '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', '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, 10, 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, 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, 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] 0 hydrogens need rotated 50 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, 4, 6, 6, 2, 2, 1, 1, 1, 2, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 23, 30, 30, 34, 34, 34, 34, 2, 2, 2, 6, 6, 6, 6, 6, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 15, 23, 34, 34, 34, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 138 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 865) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/865: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)N1CCN(C)C[C@H]1CNC(=O)OC(C)(C)C) `ZINC001566274907.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001566274907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001566274907 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1CNC(=O)OC(C)(C)C NO_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', 'N.3', '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', '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, 10, 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, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 1, 1, 1, 2, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 30, 42, 42, 44, 44, 44, 44, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 30, 44, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 156 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001566274907 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566274907 Building ZINC001566287330 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566287330' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566287330 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001566287330 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566287330/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566287330 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 866) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/866 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/866' -> `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)NC1CCN(S(=O)(=O)C(F)(F)F)CC1) `ZINC001566287330.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001566287330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566287330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001566287330 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1CCN(S(=O)(=O)C(F)(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.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 14, 11, 11, 5, 15, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 3, 3, 6, 16, 16, 16, 16, 32, 32, 32, 37, 37, 37, 16, 16, 4, 4, 4, 9, 9, 7, 9, 9, 4, 4, 4, 3, 16, 16, 16, 16, 16, 16, 16, 16, 16] 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: 178 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566287330 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566287330/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566287330 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 867) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/867 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/867' -> `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)NC1CCN(S(=O)(=O)C(F)(F)F)CC1) `ZINC001566287330.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001566287330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566287330/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001566287330 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC1CCN(S(=O)(=O)C(F)(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.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 14, 11, 11, 5, 15, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 4, 4, 6, 20, 20, 20, 20, 35, 35, 35, 37, 37, 37, 20, 20, 4, 4, 4, 10, 10, 4, 10, 10, 4, 4, 4, 4, 20, 20, 20, 20, 20, 20, 20, 20, 20] 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: 165 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566287330 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001566287330 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566287330/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566287330/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566287330 Building ZINC001566287330 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566287330' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566287330 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001566287330 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566287330/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566287330 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 866) grep: /scratch/xiaobo/418326/xbt-8058088.46/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(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1CCN(S(=O)(=O)C(F)(F)F)CC1) `ZINC001566287330.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001566287330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566287330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001566287330 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1CCN(S(=O)(=O)C(F)(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.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 14, 11, 11, 5, 15, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 3, 3, 6, 16, 16, 16, 16, 32, 32, 32, 37, 37, 37, 16, 16, 4, 4, 4, 9, 9, 7, 9, 9, 4, 4, 4, 3, 16, 16, 16, 16, 16, 16, 16, 16, 16] 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: 178 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566287330 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566287330/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566287330 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 867) grep: /scratch/xiaobo/418326/xbt-8058088.46/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(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC1CCN(S(=O)(=O)C(F)(F)F)CC1) `ZINC001566287330.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001566287330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566287330/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001566287330 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC1CCN(S(=O)(=O)C(F)(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.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 14, 11, 11, 5, 15, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 4, 4, 6, 20, 20, 20, 20, 35, 35, 35, 37, 37, 37, 20, 20, 4, 4, 4, 10, 10, 4, 10, 10, 4, 4, 4, 4, 20, 20, 20, 20, 20, 20, 20, 20, 20] 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: 165 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566287330 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001566287330 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566287330/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566287330/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566287330 Building ZINC001566337781 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566337781' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566337781 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001566337781 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566337781/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566337781 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 868) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/868 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/868' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H](O)COc1ccc(I)cc1) `ZINC001566337781.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001566337781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566337781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001566337781 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H](O)COc1ccc(I)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.3', 'H', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 12, 1, 1, 1, 1, 18, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 14, 18, 18, 17, 24, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 3, 14, 14, 54, 24, 24, 50, 50, 50, 50] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566337781 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566337781/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566337781 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 869) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/869 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/869' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@H](O)COc1ccc(I)cc1) `ZINC001566337781.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001566337781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566337781/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001566337781 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@H](O)COc1ccc(I)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.3', 'H', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 12, 1, 1, 1, 1, 18, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 13, 21, 21, 21, 29, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 13, 13, 63, 29, 29, 50, 50, 50, 50] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 239 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566337781 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001566337781 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566337781/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566337781/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566337781 Building ZINC001566337781 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566337781' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566337781 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001566337781 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566337781/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566337781 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 868) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H](O)COc1ccc(I)cc1) `ZINC001566337781.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001566337781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566337781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001566337781 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H](O)COc1ccc(I)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.3', 'H', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 12, 1, 1, 1, 1, 18, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 14, 18, 18, 17, 24, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 3, 14, 14, 54, 24, 24, 50, 50, 50, 50] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566337781 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566337781/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566337781 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 869) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@H](O)COc1ccc(I)cc1) `ZINC001566337781.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001566337781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566337781/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001566337781 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@H](O)COc1ccc(I)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.3', 'H', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 12, 1, 1, 1, 1, 18, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 13, 21, 21, 21, 29, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 13, 13, 63, 29, 29, 50, 50, 50, 50] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 239 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566337781 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001566337781 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566337781/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566337781/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566337781 Building ZINC001566337782 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566337782' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566337782 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001566337782 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566337782/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566337782 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 870) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/870 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/870' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)COc1ccc(I)cc1) `ZINC001566337782.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001566337782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566337782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001566337782 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)COc1ccc(I)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.3', 'H', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 12, 1, 1, 1, 1, 18, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 13, 21, 21, 21, 29, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 13, 13, 63, 29, 29, 50, 50, 50, 50] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 238 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566337782 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566337782/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566337782 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 871) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/871 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/871' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H](O)COc1ccc(I)cc1) `ZINC001566337782.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001566337782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566337782/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001566337782 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H](O)COc1ccc(I)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.3', 'H', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 12, 1, 1, 1, 1, 18, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 15, 19, 19, 19, 24, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 15, 15, 57, 24, 24, 50, 50, 50, 50] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566337782 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001566337782 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566337782/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566337782/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566337782 Building ZINC001566337782 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566337782' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566337782 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001566337782 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566337782/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566337782 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 870) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)COc1ccc(I)cc1) `ZINC001566337782.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001566337782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566337782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001566337782 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)COc1ccc(I)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.3', 'H', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 12, 1, 1, 1, 1, 18, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 13, 21, 21, 21, 29, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 13, 13, 63, 29, 29, 50, 50, 50, 50] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 238 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566337782 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566337782/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566337782 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 871) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H](O)COc1ccc(I)cc1) `ZINC001566337782.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001566337782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566337782/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001566337782 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H](O)COc1ccc(I)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.3', 'H', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 12, 1, 1, 1, 1, 18, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 15, 19, 19, 19, 24, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 15, 15, 57, 24, 24, 50, 50, 50, 50] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566337782 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001566337782 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566337782/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566337782/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566337782 Building ZINC001566931748 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566931748' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566931748 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001566931748 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566931748/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566931748 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 872) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/872 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/872' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)nn1c1ccc(Cl)c(Cl)c1) `ZINC001566931748.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001566931748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566931748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001566931748 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)nn1c1ccc(Cl)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', '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, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 4, 4, 4, 16, 16, 16, 16, 16, 16, 16, 4, 4, 4, 4, 2, 1, 4, 4, 1, 1, 1, 1, 16, 16, 16] 50 rigid atoms, others: [34, 5, 38, 7, 8, 9, 10, 11, 12, 16, 17, 18, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 41, 42, 43]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566931748 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566931748/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566931748 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 873) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/873 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/873' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)nn1c1ccc(Cl)c(Cl)c1) `ZINC001566931748.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001566931748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566931748/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001566931748 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)nn1c1ccc(Cl)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', '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, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 4, 4, 4, 16, 16, 16, 16, 16, 16, 16, 4, 4, 4, 4, 2, 1, 4, 4, 1, 1, 1, 1, 16, 16, 16] 50 rigid atoms, others: [34, 5, 38, 7, 8, 9, 10, 11, 12, 16, 17, 18, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 41, 42, 43]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566931748 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001566931748 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566931748/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566931748/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566931748 Building ZINC001566931748 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566931748' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566931748 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001566931748 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566931748/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566931748 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 872) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)nn1c1ccc(Cl)c(Cl)c1) `ZINC001566931748.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001566931748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566931748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001566931748 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)nn1c1ccc(Cl)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', '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, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 4, 4, 4, 16, 16, 16, 16, 16, 16, 16, 4, 4, 4, 4, 2, 1, 4, 4, 1, 1, 1, 1, 16, 16, 16] 50 rigid atoms, others: [34, 5, 38, 7, 8, 9, 10, 11, 12, 16, 17, 18, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 41, 42, 43]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566931748 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566931748/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566931748 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 873) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)nn1c1ccc(Cl)c(Cl)c1) `ZINC001566931748.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001566931748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566931748/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001566931748 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)nn1c1ccc(Cl)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', '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, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 4, 4, 4, 16, 16, 16, 16, 16, 16, 16, 4, 4, 4, 4, 2, 1, 4, 4, 1, 1, 1, 1, 16, 16, 16] 50 rigid atoms, others: [34, 5, 38, 7, 8, 9, 10, 11, 12, 16, 17, 18, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 41, 42, 43]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566931748 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001566931748 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566931748/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566931748/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001566931748 Building ZINC001567706954 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001567706954' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001567706954 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001567706954 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001567706954/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001567706954 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 874) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/874 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/874' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cccc(Br)c1OCCS(C)(=O)=O)C(=O)[C@]([O-])([SiH3])c1cccn1C) `ZINC001567706954.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001567706954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001567706954/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001567706954 none CN(Cc1cccc(Br)c1OCCS(C)(=O)=O)C(=O)[C@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 17, 1, 12, 5, 5, 14, 5, 11, 11, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 11, 17, 17, 17, 17, 17, 17, 17, 21, 31, 36, 48, 48, 48, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 11, 11, 17, 17, 17, 31, 31, 36, 36, 48, 48, 48, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001567706954 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001567706954/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001567706954 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 875) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/875 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/875' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cccc(Br)c1OCCS(C)(=O)=O)C(=O)[C@@]([O-])([SiH3])c1cccn1C) `ZINC001567706954.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001567706954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001567706954/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001567706954 none CN(Cc1cccc(Br)c1OCCS(C)(=O)=O)C(=O)[C@@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 17, 1, 12, 5, 5, 14, 5, 11, 11, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 11, 17, 17, 17, 17, 17, 17, 17, 22, 31, 36, 48, 48, 48, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 11, 11, 17, 17, 17, 31, 31, 36, 36, 48, 48, 48, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001567706954 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001567706954 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001567706954/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001567706954/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001567706954 Building ZINC001567706954 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001567706954' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001567706954 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001567706954 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001567706954/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001567706954 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 874) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CN(Cc1cccc(Br)c1OCCS(C)(=O)=O)C(=O)[C@]([O-])([SiH3])c1cccn1C) `ZINC001567706954.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001567706954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001567706954/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001567706954 none CN(Cc1cccc(Br)c1OCCS(C)(=O)=O)C(=O)[C@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 17, 1, 12, 5, 5, 14, 5, 11, 11, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 11, 17, 17, 17, 17, 17, 17, 17, 21, 31, 36, 48, 48, 48, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 11, 11, 17, 17, 17, 31, 31, 36, 36, 48, 48, 48, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001567706954 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001567706954/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001567706954 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 875) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CN(Cc1cccc(Br)c1OCCS(C)(=O)=O)C(=O)[C@@]([O-])([SiH3])c1cccn1C) `ZINC001567706954.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001567706954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001567706954/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001567706954 none CN(Cc1cccc(Br)c1OCCS(C)(=O)=O)C(=O)[C@@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 17, 1, 12, 5, 5, 14, 5, 11, 11, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 11, 17, 17, 17, 17, 17, 17, 17, 22, 31, 36, 48, 48, 48, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 11, 11, 17, 17, 17, 31, 31, 36, 36, 48, 48, 48, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001567706954 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001567706954 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001567706954/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001567706954/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001567706954 Building ZINC001568128366 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568128366' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568128366 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001568128366 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568128366/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568128366 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 876) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/876 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/876' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC(c2ccc(Br)cc2)CC1) `ZINC001568128366.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001568128366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568128366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001568128366 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC(c2ccc(Br)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 3, 1, 1, 1, 1, 5, 9, 12, 12, 12, 12, 14, 14, 14, 14, 14, 14, 12, 12, 3, 3, 3, 3, 10, 10, 3, 12, 12, 12, 12, 12, 14, 14, 14, 14, 12, 12, 12, 12] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568128366 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568128366/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568128366 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 877) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/877 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/877' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC(c2ccc(Br)cc2)CC1) `ZINC001568128366.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001568128366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568128366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001568128366 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC(c2ccc(Br)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 7, 2, 1, 1, 1, 1, 4, 10, 14, 14, 14, 14, 15, 15, 15, 15, 15, 15, 14, 14, 2, 2, 2, 2, 7, 7, 2, 14, 14, 14, 14, 14, 15, 15, 15, 15, 14, 14, 14, 14] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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/418326/xbt-8058088.46/working/building/ZINC001568128366 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001568128366 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568128366/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568128366/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568128366 Building ZINC001568128366 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568128366' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568128366 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001568128366 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568128366/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568128366 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 876) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC(c2ccc(Br)cc2)CC1) `ZINC001568128366.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001568128366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568128366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001568128366 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC(c2ccc(Br)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 3, 1, 1, 1, 1, 5, 9, 12, 12, 12, 12, 14, 14, 14, 14, 14, 14, 12, 12, 3, 3, 3, 3, 10, 10, 3, 12, 12, 12, 12, 12, 14, 14, 14, 14, 12, 12, 12, 12] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568128366 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568128366/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568128366 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 877) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC(c2ccc(Br)cc2)CC1) `ZINC001568128366.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001568128366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568128366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001568128366 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC(c2ccc(Br)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 7, 2, 1, 1, 1, 1, 4, 10, 14, 14, 14, 14, 15, 15, 15, 15, 15, 15, 14, 14, 2, 2, 2, 2, 7, 7, 2, 14, 14, 14, 14, 14, 15, 15, 15, 15, 14, 14, 14, 14] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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/418326/xbt-8058088.46/working/building/ZINC001568128366 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001568128366 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568128366/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568128366/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568128366 Building ZINC001568809865 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568809865' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568809865 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001568809865 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568809865/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568809865 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 878) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/878 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/878' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCNC(=O)[C@@H](C)OC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1) `ZINC001568809865.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001568809865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568809865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001568809865 none COCCNC(=O)[C@@H](C)OC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', '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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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, 5, 5, 8, 1, 11, 5, 7, 5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 5, 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: [32, 32, 29, 17, 17, 15, 17, 15, 15, 15, 15, 9, 15, 9, 9, 9, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 32, 32, 32, 32, 32, 29, 29, 17, 15, 15, 15, 9, 9, 3, 4, 4, 4, 4, 9, 9] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568809865 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568809865/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568809865 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 879) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/879 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/879' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCNC(=O)[C@@H](C)OC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1) `ZINC001568809865.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001568809865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568809865/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001568809865 none COCCNC(=O)[C@@H](C)OC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', '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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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, 5, 5, 8, 1, 11, 5, 7, 5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 5, 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: [33, 33, 31, 16, 16, 14, 16, 14, 14, 14, 13, 5, 14, 5, 9, 9, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 33, 33, 33, 33, 33, 31, 31, 16, 14, 14, 14, 9, 9, 3, 4, 4, 4, 4, 9, 9] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568809865 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001568809865 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568809865/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568809865/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568809865 Building ZINC001568809865 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568809865' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568809865 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001568809865 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568809865/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568809865 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 878) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COCCNC(=O)[C@@H](C)OC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1) `ZINC001568809865.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001568809865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568809865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001568809865 none COCCNC(=O)[C@@H](C)OC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', '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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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, 5, 5, 8, 1, 11, 5, 7, 5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 5, 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: [32, 32, 29, 17, 17, 15, 17, 15, 15, 15, 15, 9, 15, 9, 9, 9, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 32, 32, 32, 32, 32, 29, 29, 17, 15, 15, 15, 9, 9, 3, 4, 4, 4, 4, 9, 9] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568809865 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568809865/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568809865 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 879) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COCCNC(=O)[C@@H](C)OC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1) `ZINC001568809865.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001568809865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568809865/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001568809865 none COCCNC(=O)[C@@H](C)OC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', '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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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, 5, 5, 8, 1, 11, 5, 7, 5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 5, 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: [33, 33, 31, 16, 16, 14, 16, 14, 14, 14, 13, 5, 14, 5, 9, 9, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 33, 33, 33, 33, 33, 31, 31, 16, 14, 14, 14, 9, 9, 3, 4, 4, 4, 4, 9, 9] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568809865 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001568809865 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568809865/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568809865/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568809865 Building ZINC001568809866 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568809866' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568809866 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001568809866 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568809866/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568809866 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 880) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/880 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/880' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCNC(=O)[C@H](C)OC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1) `ZINC001568809866.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001568809866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568809866/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001568809866 none COCCNC(=O)[C@H](C)OC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', '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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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, 5, 5, 8, 1, 11, 5, 7, 5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 5, 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: [32, 32, 31, 17, 17, 15, 17, 14, 15, 15, 14, 9, 14, 3, 9, 9, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 32, 32, 32, 32, 32, 31, 31, 17, 15, 15, 15, 9, 9, 3, 4, 4, 4, 4, 9, 9] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568809866 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568809866/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568809866 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 881) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/881 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/881' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCNC(=O)[C@H](C)OC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1) `ZINC001568809866.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001568809866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568809866/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001568809866 none COCCNC(=O)[C@H](C)OC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', '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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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, 5, 5, 8, 1, 11, 5, 7, 5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 5, 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: [32, 32, 29, 17, 16, 15, 17, 15, 15, 15, 13, 3, 14, 3, 9, 9, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 32, 32, 32, 32, 32, 30, 30, 16, 15, 15, 15, 9, 9, 3, 4, 4, 4, 4, 9, 9] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568809866 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001568809866 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568809866/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568809866/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568809866 Building ZINC001568809866 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568809866' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568809866 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001568809866 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568809866/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568809866 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 880) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COCCNC(=O)[C@H](C)OC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1) `ZINC001568809866.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001568809866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568809866/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001568809866 none COCCNC(=O)[C@H](C)OC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', '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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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, 5, 5, 8, 1, 11, 5, 7, 5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 5, 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: [32, 32, 31, 17, 17, 15, 17, 14, 15, 15, 14, 9, 14, 3, 9, 9, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 32, 32, 32, 32, 32, 31, 31, 17, 15, 15, 15, 9, 9, 3, 4, 4, 4, 4, 9, 9] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568809866 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568809866/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568809866 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 881) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COCCNC(=O)[C@H](C)OC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1) `ZINC001568809866.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001568809866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568809866/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001568809866 none COCCNC(=O)[C@H](C)OC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', '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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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, 5, 5, 8, 1, 11, 5, 7, 5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 5, 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: [32, 32, 29, 17, 16, 15, 17, 15, 15, 15, 13, 3, 14, 3, 9, 9, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 32, 32, 32, 32, 32, 30, 30, 16, 15, 15, 15, 9, 9, 3, 4, 4, 4, 4, 9, 9] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568809866 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001568809866 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568809866/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568809866/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001568809866 Building ZINC001569333640 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569333640' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569333640 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001569333640 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569333640/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569333640 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 882) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/882 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/882' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CNS(C)(=O)=O)cc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001569333640.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001569333640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569333640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001569333640 none COc1ccc(CNS(C)(=O)=O)cc1NC(=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.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 5, 11, 11, 1, 1, 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, 6, 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, 4, 7, 7, 6, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 2, 2, 2, 2, 2, 8, 27, 29, 29, 29, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 3, 3, 3, 2, 2, 8, 8, 27, 29, 29, 29, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569333640 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569333640/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569333640 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 883) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/883 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/883' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CNS(C)(=O)=O)cc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001569333640.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001569333640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569333640/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001569333640 none COc1ccc(CNS(C)(=O)=O)cc1NC(=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.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 5, 11, 11, 1, 1, 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, 6, 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, 4, 7, 7, 6, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 2, 2, 2, 2, 2, 8, 27, 29, 29, 29, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 3, 4, 4, 2, 2, 3, 3, 3, 2, 2, 8, 8, 27, 29, 29, 29, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569333640 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001569333640 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569333640/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569333640/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569333640 Building ZINC001569333640 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569333640' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569333640 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001569333640 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569333640/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569333640 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 882) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc(CNS(C)(=O)=O)cc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001569333640.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001569333640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569333640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001569333640 none COc1ccc(CNS(C)(=O)=O)cc1NC(=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.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 5, 11, 11, 1, 1, 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, 6, 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, 4, 7, 7, 6, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 2, 2, 2, 2, 2, 8, 27, 29, 29, 29, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 3, 3, 3, 2, 2, 8, 8, 27, 29, 29, 29, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569333640 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569333640/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569333640 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 883) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc(CNS(C)(=O)=O)cc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001569333640.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001569333640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569333640/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001569333640 none COc1ccc(CNS(C)(=O)=O)cc1NC(=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.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 5, 11, 11, 1, 1, 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, 6, 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, 4, 7, 7, 6, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 2, 2, 2, 2, 2, 8, 27, 29, 29, 29, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 3, 4, 4, 2, 2, 3, 3, 3, 2, 2, 8, 8, 27, 29, 29, 29, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569333640 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001569333640 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569333640/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569333640/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569333640 Building ZINC001569699629 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569699629' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569699629 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001569699629 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569699629/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569699629 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 884) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/884 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/884' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1c2cccc(Br)c2CC1(C)C) `ZINC001569699629.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001569699629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569699629/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001569699629 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1c2cccc(Br)c2CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 17, 1, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 9, 3, 1, 1, 1, 1, 3, 3, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 3, 9, 9, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569699629 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569699629/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569699629 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 885) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/885 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/885' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1c2cccc(Br)c2CC1(C)C) `ZINC001569699629.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001569699629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569699629/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001569699629 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1c2cccc(Br)c2CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 17, 1, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 10, 10, 10, 4, 1, 1, 1, 1, 4, 4, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 4, 10, 10, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569699629 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001569699629 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569699629/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569699629/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569699629 Building ZINC001569699629 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569699629' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569699629 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001569699629 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569699629/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569699629 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 884) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1c2cccc(Br)c2CC1(C)C) `ZINC001569699629.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001569699629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569699629/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001569699629 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1c2cccc(Br)c2CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 17, 1, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 9, 3, 1, 1, 1, 1, 3, 3, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 3, 9, 9, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569699629 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569699629/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569699629 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 885) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1c2cccc(Br)c2CC1(C)C) `ZINC001569699629.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001569699629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569699629/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001569699629 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1c2cccc(Br)c2CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 17, 1, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 10, 10, 10, 4, 1, 1, 1, 1, 4, 4, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 4, 10, 10, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569699629 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001569699629 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569699629/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569699629/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569699629 Building ZINC001569699630 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569699630' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569699630 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001569699630 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569699630/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569699630 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 886) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/886 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/886' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1c2cccc(Br)c2CC1(C)C) `ZINC001569699630.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001569699630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569699630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001569699630 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1c2cccc(Br)c2CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 17, 1, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 10, 10, 10, 4, 1, 1, 1, 1, 4, 4, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 4, 10, 10, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569699630 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569699630/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569699630 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 887) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/887 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/887' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1c2cccc(Br)c2CC1(C)C) `ZINC001569699630.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001569699630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569699630/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001569699630 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1c2cccc(Br)c2CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 17, 1, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 9, 3, 1, 1, 1, 1, 3, 3, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 3, 9, 9, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569699630 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001569699630 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569699630/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569699630/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569699630 Building ZINC001569699630 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569699630' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569699630 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001569699630 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569699630/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569699630 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 886) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1c2cccc(Br)c2CC1(C)C) `ZINC001569699630.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001569699630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569699630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001569699630 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1c2cccc(Br)c2CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 17, 1, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 10, 10, 10, 4, 1, 1, 1, 1, 4, 4, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 4, 10, 10, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569699630 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569699630/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569699630 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 887) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1c2cccc(Br)c2CC1(C)C) `ZINC001569699630.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001569699630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569699630/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001569699630 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1c2cccc(Br)c2CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 17, 1, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 9, 3, 1, 1, 1, 1, 3, 3, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 3, 9, 9, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569699630 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001569699630 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569699630/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569699630/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001569699630 Building ZINC001583535118 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001583535118' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001583535118 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583535118 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001583535118/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001583535118 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 888) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/888 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/888' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)c1ccc(OC)c(Br)c1) `ZINC001583535118.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583535118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001583535118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001583535118 none CCOC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)c1ccc(OC)c(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 1, 12, 5, 1, 17, 1, 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, 3, 7, 5, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 8, 8, 3, 8, 2, 3, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 6, 12, 27, 15, 15, 15, 15, 15, 15, 15, 15, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 27, 27, 27, 15] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001583535118 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001583535118/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001583535118 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 889) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/889 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/889' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)c1ccc(OC)c(Br)c1) `ZINC001583535118.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583535118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001583535118/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001583535118 none CCOC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)c1ccc(OC)c(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 1, 12, 5, 1, 17, 1, 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, 3, 7, 5, 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, 7, 7] 0 hydrogens 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, 4, 5, 2, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 8, 12, 24, 12, 12, 12, 10, 10, 10, 10, 10, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 24, 24, 24, 12] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001583535118 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001583535118 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001583535118/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001583535118/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001583535118 Building ZINC001583535118 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001583535118' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001583535118 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583535118 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001583535118/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001583535118 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 888) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCOC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)c1ccc(OC)c(Br)c1) `ZINC001583535118.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583535118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001583535118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001583535118 none CCOC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)c1ccc(OC)c(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 1, 12, 5, 1, 17, 1, 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, 3, 7, 5, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 8, 8, 3, 8, 2, 3, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 6, 12, 27, 15, 15, 15, 15, 15, 15, 15, 15, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 27, 27, 27, 15] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001583535118 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001583535118/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001583535118 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 889) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCOC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)c1ccc(OC)c(Br)c1) `ZINC001583535118.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583535118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001583535118/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001583535118 none CCOC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)c1ccc(OC)c(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 1, 12, 5, 1, 17, 1, 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, 3, 7, 5, 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, 7, 7] 0 hydrogens 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, 4, 5, 2, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 8, 12, 24, 12, 12, 12, 10, 10, 10, 10, 10, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 24, 24, 24, 12] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001583535118 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001583535118 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001583535118/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001583535118/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001583535118 Building ZINC001583535119 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001583535119' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001583535119 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583535119 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001583535119/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001583535119 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 890) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/890 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/890' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)c1ccc(OC)c(Br)c1) `ZINC001583535119.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583535119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001583535119/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001583535119 none CCOC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)c1ccc(OC)c(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 1, 12, 5, 1, 17, 1, 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, 3, 7, 5, 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, 7, 7] 0 hydrogens 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, 5, 3, 5, 2, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 3, 12, 12, 6, 8, 26, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 26, 26, 26, 12] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 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/418326/xbt-8058088.46/working/building/ZINC001583535119 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001583535119/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001583535119 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 891) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/891 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/891' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)c1ccc(OC)c(Br)c1) `ZINC001583535119.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583535119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001583535119/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001583535119 none CCOC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)c1ccc(OC)c(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 1, 12, 5, 1, 17, 1, 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, 3, 7, 5, 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, 7, 7] 0 hydrogens 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, 3, 7, 2, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 3, 15, 15, 6, 15, 24, 15, 15, 15, 13, 13, 13, 13, 13, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 15, 15, 24, 24, 24, 15] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001583535119 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001583535119 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001583535119/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001583535119/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001583535119 Building ZINC001583535119 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001583535119' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001583535119 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001583535119 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001583535119/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001583535119 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 890) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCOC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)c1ccc(OC)c(Br)c1) `ZINC001583535119.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001583535119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001583535119/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001583535119 none CCOC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)c1ccc(OC)c(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 1, 12, 5, 1, 17, 1, 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, 3, 7, 5, 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, 7, 7] 0 hydrogens 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, 5, 3, 5, 2, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 3, 12, 12, 6, 8, 26, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 26, 26, 26, 12] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 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/418326/xbt-8058088.46/working/building/ZINC001583535119 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001583535119/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001583535119 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 891) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCOC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)c1ccc(OC)c(Br)c1) `ZINC001583535119.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001583535119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001583535119/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001583535119 none CCOC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)c1ccc(OC)c(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 1, 12, 5, 1, 17, 1, 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, 3, 7, 5, 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, 7, 7] 0 hydrogens 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, 3, 7, 2, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 3, 15, 15, 6, 15, 24, 15, 15, 15, 13, 13, 13, 13, 13, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 15, 15, 24, 24, 24, 15] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001583535119 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001583535119 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001583535119/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001583535119/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001583535119 Building ZINC001584013832 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584013832' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584013832 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584013832 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584013832/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584013832 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 892) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/892 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/892' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@]2(CC(=O)NN2C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC001584013832.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584013832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584013832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001584013832 none CC(C)(C)OC(=O)N1CC[C@]2(CC(=O)NN2C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)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', 'C.2', 'O.2', 'N.am', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 15, 25, 15, 15, 15, 15, 15, 15, 15, 15, 7, 2, 9, 1, 1, 1, 4, 4, 4, 4, 4, 15, 37, 37, 37, 37, 37, 37, 37, 37, 37, 15, 15, 15, 15, 15, 15, 15, 4, 4, 15, 15] 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: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584013832 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584013832/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584013832 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 893) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/893 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/893' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@]2(CC(=O)NN2C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC001584013832.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584013832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584013832/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001584013832 none CC(C)(C)OC(=O)N1CC[C@]2(CC(=O)NN2C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)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', 'C.2', 'O.2', 'N.am', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 14, 24, 14, 14, 14, 14, 14, 14, 14, 14, 6, 1, 10, 1, 1, 1, 4, 4, 4, 4, 4, 14, 37, 37, 37, 37, 37, 37, 37, 37, 37, 14, 14, 14, 14, 14, 14, 14, 4, 4, 14, 14] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584013832 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001584013832 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584013832/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584013832/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584013832 Building ZINC001584013832 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584013832' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584013832 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584013832 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584013832/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584013832 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 892) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC(C)(C)OC(=O)N1CC[C@]2(CC(=O)NN2C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC001584013832.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584013832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584013832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001584013832 none CC(C)(C)OC(=O)N1CC[C@]2(CC(=O)NN2C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)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', 'C.2', 'O.2', 'N.am', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 15, 25, 15, 15, 15, 15, 15, 15, 15, 15, 7, 2, 9, 1, 1, 1, 4, 4, 4, 4, 4, 15, 37, 37, 37, 37, 37, 37, 37, 37, 37, 15, 15, 15, 15, 15, 15, 15, 4, 4, 15, 15] 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: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584013832 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584013832/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584013832 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 893) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC(C)(C)OC(=O)N1CC[C@]2(CC(=O)NN2C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC001584013832.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584013832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584013832/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001584013832 none CC(C)(C)OC(=O)N1CC[C@]2(CC(=O)NN2C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)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', 'C.2', 'O.2', 'N.am', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 14, 24, 14, 14, 14, 14, 14, 14, 14, 14, 6, 1, 10, 1, 1, 1, 4, 4, 4, 4, 4, 14, 37, 37, 37, 37, 37, 37, 37, 37, 37, 14, 14, 14, 14, 14, 14, 14, 4, 4, 14, 14] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584013832 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001584013832 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584013832/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584013832/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584013832 Building ZINC001584013833 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584013833' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584013833 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584013833 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584013833/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584013833 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 894) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/894 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/894' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@]2(CC(=O)NN2C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC001584013833.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584013833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584013833/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001584013833 none CC(C)(C)OC(=O)N1CC[C@@]2(CC(=O)NN2C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)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', 'C.2', 'O.2', 'N.am', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 13, 24, 13, 13, 13, 13, 13, 13, 13, 13, 5, 1, 7, 1, 1, 1, 4, 4, 4, 4, 4, 13, 37, 37, 37, 37, 37, 37, 37, 37, 37, 13, 13, 13, 13, 13, 13, 13, 4, 4, 13, 13] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584013833 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584013833/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584013833 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 895) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/895 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/895' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@]2(CC(=O)NN2C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC001584013833.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584013833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584013833/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001584013833 none CC(C)(C)OC(=O)N1CC[C@@]2(CC(=O)NN2C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)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', 'C.2', 'O.2', 'N.am', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 15, 26, 15, 15, 15, 15, 15, 15, 15, 15, 7, 2, 9, 1, 1, 1, 4, 4, 4, 4, 4, 15, 38, 38, 38, 38, 38, 38, 38, 38, 38, 15, 15, 15, 15, 15, 15, 15, 4, 4, 15, 15] 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: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584013833 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001584013833 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584013833/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584013833/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584013833 Building ZINC001584013833 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584013833' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584013833 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584013833 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584013833/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584013833 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 894) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC(C)(C)OC(=O)N1CC[C@@]2(CC(=O)NN2C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC001584013833.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584013833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584013833/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001584013833 none CC(C)(C)OC(=O)N1CC[C@@]2(CC(=O)NN2C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)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', 'C.2', 'O.2', 'N.am', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 13, 24, 13, 13, 13, 13, 13, 13, 13, 13, 5, 1, 7, 1, 1, 1, 4, 4, 4, 4, 4, 13, 37, 37, 37, 37, 37, 37, 37, 37, 37, 13, 13, 13, 13, 13, 13, 13, 4, 4, 13, 13] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584013833 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584013833/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584013833 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 895) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC(C)(C)OC(=O)N1CC[C@@]2(CC(=O)NN2C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC001584013833.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584013833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584013833/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001584013833 none CC(C)(C)OC(=O)N1CC[C@@]2(CC(=O)NN2C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)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', 'C.2', 'O.2', 'N.am', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 15, 26, 15, 15, 15, 15, 15, 15, 15, 15, 7, 2, 9, 1, 1, 1, 4, 4, 4, 4, 4, 15, 38, 38, 38, 38, 38, 38, 38, 38, 38, 15, 15, 15, 15, 15, 15, 15, 4, 4, 15, 15] 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: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584013833 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001584013833 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584013833/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584013833/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584013833 Building ZINC001584103562 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584103562' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584103562 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584103562 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584103562/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584103562 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 896) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/896 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/896' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CC1)Nc1ccc(Cl)cc1) `ZINC001584103562.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584103562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584103562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001584103562 none O=C(CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CC1)Nc1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 8, 8, 8, 8, 4, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 26, 26, 31, 31, 29, 30, 31, 31, 18, 18, 8, 8, 8, 8, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 26, 31, 31, 31, 31] 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584103562 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584103562/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584103562 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 897) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/897 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/897' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CC1)Nc1ccc(Cl)cc1) `ZINC001584103562.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584103562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584103562/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001584103562 none O=C(CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CC1)Nc1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 19, 8, 8, 8, 8, 4, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 27, 27, 35, 35, 28, 33, 35, 35, 19, 19, 8, 8, 8, 8, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 27, 35, 35, 35, 35] 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]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584103562 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001584103562 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584103562/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584103562/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584103562 Building ZINC001584103562 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584103562' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584103562 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584103562 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584103562/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584103562 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 896) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: O=C(CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CC1)Nc1ccc(Cl)cc1) `ZINC001584103562.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584103562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584103562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001584103562 none O=C(CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CC1)Nc1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 8, 8, 8, 8, 4, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 26, 26, 31, 31, 29, 30, 31, 31, 18, 18, 8, 8, 8, 8, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 26, 31, 31, 31, 31] 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584103562 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584103562/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584103562 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 897) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: O=C(CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CC1)Nc1ccc(Cl)cc1) `ZINC001584103562.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584103562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584103562/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001584103562 none O=C(CN1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CC1)Nc1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 19, 8, 8, 8, 8, 4, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 27, 27, 35, 35, 28, 33, 35, 35, 19, 19, 8, 8, 8, 8, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 27, 35, 35, 35, 35] 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]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584103562 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001584103562 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584103562/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584103562/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584103562 Building ZINC001584217669 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584217669' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584217669 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584217669 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584217669/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584217669 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 898) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/898 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/898' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001584217669.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584217669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584217669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001584217669 none COC(=O)C[C@H]1COCCN1C(=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.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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, 12, 1, 11, 5, 5, 7, 5, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 3, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 14, 14, 4, 14, 14, 14, 14, 14, 14, 2, 2, 12, 12, 12, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 14, 4, 14, 2, 2, 2] 50 rigid atoms, others: [43, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 40, 41, 39, 38, 42] set([0, 1, 2, 3, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 68 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584217669 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584217669/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584217669 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 899) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/899 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/899' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001584217669.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584217669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584217669/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001584217669 none COC(=O)C[C@H]1COCCN1C(=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.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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, 12, 1, 11, 5, 5, 7, 5, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 5, 10, 2, 2, 2, 2, 2, 2, 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, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2] 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584217669 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001584217669 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584217669/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584217669/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584217669 Building ZINC001584217669 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584217669' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584217669 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584217669 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584217669/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584217669 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 898) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COC(=O)C[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001584217669.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584217669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584217669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001584217669 none COC(=O)C[C@H]1COCCN1C(=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.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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, 12, 1, 11, 5, 5, 7, 5, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 3, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 14, 14, 4, 14, 14, 14, 14, 14, 14, 2, 2, 12, 12, 12, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 14, 4, 14, 2, 2, 2] 50 rigid atoms, others: [43, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 40, 41, 39, 38, 42] set([0, 1, 2, 3, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 68 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584217669 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584217669/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584217669 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 899) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COC(=O)C[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001584217669.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584217669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584217669/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001584217669 none COC(=O)C[C@H]1COCCN1C(=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.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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, 12, 1, 11, 5, 5, 7, 5, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 5, 10, 2, 2, 2, 2, 2, 2, 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, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2] 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584217669 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001584217669 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584217669/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584217669/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584217669 Building ZINC001584217670 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584217670' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584217670 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584217670 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584217670/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584217670 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 900) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/900 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/900' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001584217670.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584217670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584217670/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001584217670 none COC(=O)C[C@@H]1COCCN1C(=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.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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, 12, 1, 11, 5, 5, 7, 5, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 5, 10, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 4, 10, 10, 10, 10, 10, 10, 2, 2, 10, 10, 10, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 6, 10, 2, 2, 2] 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]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584217670 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584217670/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584217670 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 901) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/901 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/901' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001584217670.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584217670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584217670/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001584217670 none COC(=O)C[C@@H]1COCCN1C(=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.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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, 12, 1, 11, 5, 5, 7, 5, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 3, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 4, 12, 12, 12, 12, 12, 12, 2, 2, 10, 10, 10, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 12, 4, 12, 2, 2, 2] 50 rigid atoms, others: [43, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 40, 41, 39, 38, 42] set([0, 1, 2, 3, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584217670 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001584217670 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584217670/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584217670/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584217670 Building ZINC001584217670 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584217670' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584217670 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584217670 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584217670/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584217670 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 900) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COC(=O)C[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001584217670.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584217670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584217670/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001584217670 none COC(=O)C[C@@H]1COCCN1C(=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.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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, 12, 1, 11, 5, 5, 7, 5, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 5, 10, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 4, 10, 10, 10, 10, 10, 10, 2, 2, 10, 10, 10, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 6, 10, 2, 2, 2] 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]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584217670 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584217670/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584217670 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 901) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COC(=O)C[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001584217670.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584217670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584217670/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001584217670 none COC(=O)C[C@@H]1COCCN1C(=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.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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, 12, 1, 11, 5, 5, 7, 5, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 3, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 4, 12, 12, 12, 12, 12, 12, 2, 2, 10, 10, 10, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 12, 4, 12, 2, 2, 2] 50 rigid atoms, others: [43, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 40, 41, 39, 38, 42] set([0, 1, 2, 3, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584217670 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001584217670 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584217670/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584217670/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584217670 Building ZINC001584352012 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584352012' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584352012 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584352012 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584352012/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584352012 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 902) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/902 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/902' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)N1CCN(c2ccc(Cl)cc2)CC1) `ZINC001584352012.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584352012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584352012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001584352012 none O=C(CNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)N1CCN(c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', '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', 'N.am', 'C.3', 'C.3', 'N.pl3', '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, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 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: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 29, 31, 31, 29, 29, 31, 31, 29, 29, 12, 12, 4, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 31, 31, 31, 31, 29, 29, 29, 29] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 94 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584352012 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584352012/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584352012 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 903) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/903 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/903' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)N1CCN(c2ccc(Cl)cc2)CC1) `ZINC001584352012.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584352012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584352012/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001584352012 none O=C(CNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)N1CCN(c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', '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', 'N.am', 'C.3', 'C.3', 'N.pl3', '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, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 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: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 29, 31, 31, 29, 29, 31, 31, 29, 29, 13, 13, 4, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 31, 31, 31, 31, 29, 29, 29, 29] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 99 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584352012 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001584352012 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584352012/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584352012/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584352012 Building ZINC001584352012 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584352012' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584352012 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001584352012 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584352012/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584352012 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 902) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: O=C(CNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)N1CCN(c2ccc(Cl)cc2)CC1) `ZINC001584352012.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584352012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584352012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001584352012 none O=C(CNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)N1CCN(c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', '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', 'N.am', 'C.3', 'C.3', 'N.pl3', '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, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 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: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 29, 31, 31, 29, 29, 31, 31, 29, 29, 12, 12, 4, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 31, 31, 31, 31, 29, 29, 29, 29] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 94 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584352012 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584352012/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584352012 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 903) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: O=C(CNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)N1CCN(c2ccc(Cl)cc2)CC1) `ZINC001584352012.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584352012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584352012/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001584352012 none O=C(CNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)N1CCN(c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', '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', 'N.am', 'C.3', 'C.3', 'N.pl3', '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, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 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: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 29, 31, 31, 29, 29, 31, 31, 29, 29, 13, 13, 4, 5, 5, 5, 5, 5, 5, 5, 29, 29, 29, 29, 31, 31, 31, 31, 29, 29, 29, 29] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 99 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584352012 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001584352012 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584352012/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584352012/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584352012 Building ZINC001584792192 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001584792192 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 904) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/904 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/904' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCCN(S(=O)(=O)c2cccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)CC1) `ZINC001584792192.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584792192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001584792192 none CN1CCCN(S(=O)(=O)c2cccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'F', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 24, 7, 15, 15, 7, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 7, 7, 7, 3, 6, 6, 6, 6, 7, 33, 33, 33, 33] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 905) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/905 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/905' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCCN(S(=O)(=O)c2cccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)CC1) `ZINC001584792192.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584792192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001584792192 none CN1CCCN(S(=O)(=O)c2cccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'F', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 24, 7, 15, 15, 7, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 7, 7, 7, 3, 6, 6, 6, 6, 7, 33, 33, 33, 33] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 906) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/906 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/906' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCCN(S(=O)(=O)c2cccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)CC1) `ZINC001584792192.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001584792192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001584792192 none CN1CCCN(S(=O)(=O)c2cccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'F', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 6, 13, 13, 6, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 6, 6, 6, 3, 6, 6, 6, 6, 6, 31, 31, 31, 31] 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: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 907) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/907 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/907' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCCN(S(=O)(=O)c2cccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)CC1) `ZINC001584792192.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001584792192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001584792192 none CN1CCCN(S(=O)(=O)c2cccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'F', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 6, 13, 13, 6, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 6, 6, 6, 3, 6, 6, 6, 6, 6, 31, 31, 31, 31] 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: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001584792192 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192 Building ZINC001584792192 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001584792192 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 904) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CN1CCCN(S(=O)(=O)c2cccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)CC1) `ZINC001584792192.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584792192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001584792192 none CN1CCCN(S(=O)(=O)c2cccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'F', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 24, 7, 15, 15, 7, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 7, 7, 7, 3, 6, 6, 6, 6, 7, 33, 33, 33, 33] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 905) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CN1CCCN(S(=O)(=O)c2cccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)CC1) `ZINC001584792192.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584792192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001584792192 none CN1CCCN(S(=O)(=O)c2cccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'F', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 24, 7, 15, 15, 7, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 7, 7, 7, 3, 6, 6, 6, 6, 7, 33, 33, 33, 33] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 906) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/906: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCCN(S(=O)(=O)c2cccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)CC1) `ZINC001584792192.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001584792192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001584792192 none CN1CCCN(S(=O)(=O)c2cccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'F', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 6, 13, 13, 6, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 6, 6, 6, 3, 6, 6, 6, 6, 6, 31, 31, 31, 31] 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: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 907) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/907: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCCN(S(=O)(=O)c2cccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)CC1) `ZINC001584792192.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001584792192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001584792192 none CN1CCCN(S(=O)(=O)c2cccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'F', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 6, 13, 13, 6, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 6, 6, 6, 3, 6, 6, 6, 6, 6, 31, 31, 31, 31] 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: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001584792192 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192 Building ZINC001584792192 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001584792192 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 904) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CN1CCCN(S(=O)(=O)c2cccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)CC1) `ZINC001584792192.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584792192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001584792192 none CN1CCCN(S(=O)(=O)c2cccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'F', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 24, 7, 15, 15, 7, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 7, 7, 7, 3, 6, 6, 6, 6, 7, 33, 33, 33, 33] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 905) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CN1CCCN(S(=O)(=O)c2cccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)CC1) `ZINC001584792192.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584792192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001584792192 none CN1CCCN(S(=O)(=O)c2cccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'F', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 24, 7, 15, 15, 7, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 7, 7, 7, 3, 6, 6, 6, 6, 7, 33, 33, 33, 33] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 906) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/906: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCCN(S(=O)(=O)c2cccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)CC1) `ZINC001584792192.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001584792192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001584792192 none CN1CCCN(S(=O)(=O)c2cccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'F', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 6, 13, 13, 6, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 6, 6, 6, 3, 6, 6, 6, 6, 6, 31, 31, 31, 31] 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: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 907) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/907: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCCN(S(=O)(=O)c2cccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)CC1) `ZINC001584792192.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001584792192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001584792192 none CN1CCCN(S(=O)(=O)c2cccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'F', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 6, 13, 13, 6, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 6, 6, 6, 3, 6, 6, 6, 6, 6, 31, 31, 31, 31] 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: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001584792192 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192 Building ZINC001584792192 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001584792192 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 904) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CN1CCCN(S(=O)(=O)c2cccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)CC1) `ZINC001584792192.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001584792192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001584792192 none CN1CCCN(S(=O)(=O)c2cccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'F', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 24, 7, 15, 15, 7, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 7, 7, 7, 3, 6, 6, 6, 6, 7, 33, 33, 33, 33] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 905) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CN1CCCN(S(=O)(=O)c2cccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)CC1) `ZINC001584792192.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001584792192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001584792192 none CN1CCCN(S(=O)(=O)c2cccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'F', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 24, 7, 15, 15, 7, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 7, 7, 7, 3, 6, 6, 6, 6, 7, 33, 33, 33, 33] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 906) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/906: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCCN(S(=O)(=O)c2cccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)CC1) `ZINC001584792192.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001584792192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001584792192 none CN1CCCN(S(=O)(=O)c2cccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'F', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 6, 13, 13, 6, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 6, 6, 6, 3, 6, 6, 6, 6, 6, 31, 31, 31, 31] 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: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 907) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/907: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCCN(S(=O)(=O)c2cccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)CC1) `ZINC001584792192.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001584792192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001584792192 none CN1CCCN(S(=O)(=O)c2cccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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', 'F', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 6, 13, 13, 6, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 6, 6, 6, 3, 6, 6, 6, 6, 6, 31, 31, 31, 31] 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: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001584792192 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001584792192 Building ZINC001585155463 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001585155463' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001585155463 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585155463 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001585155463/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001585155463 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 908) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/908 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/908' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCCc2cc(Br)ccc21) `ZINC001585155463.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585155463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001585155463/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001585155463 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCCc2cc(Br)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 1, 1, 1, 17, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 11, 4, 1, 1, 1, 1, 4, 4, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4, 4, 4, 11, 11, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001585155463 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001585155463/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001585155463 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 909) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/909 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/909' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCCc2cc(Br)ccc21) `ZINC001585155463.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585155463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001585155463/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001585155463 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCCc2cc(Br)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 1, 1, 1, 17, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 11, 11, 5, 1, 1, 1, 1, 3, 3, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 5, 5, 5, 11, 11, 5, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001585155463 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001585155463 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001585155463/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001585155463/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001585155463 Building ZINC001585155463 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001585155463' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001585155463 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585155463 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001585155463/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001585155463 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 908) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCCc2cc(Br)ccc21) `ZINC001585155463.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585155463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001585155463/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001585155463 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCCc2cc(Br)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 1, 1, 1, 17, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 11, 4, 1, 1, 1, 1, 4, 4, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4, 4, 4, 11, 11, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001585155463 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001585155463/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001585155463 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 909) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCCc2cc(Br)ccc21) `ZINC001585155463.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585155463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001585155463/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001585155463 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCCc2cc(Br)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 1, 1, 1, 17, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 11, 11, 5, 1, 1, 1, 1, 3, 3, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 5, 5, 5, 11, 11, 5, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001585155463 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001585155463 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001585155463/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001585155463/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001585155463 Building ZINC001585155464 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001585155464' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001585155464 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585155464 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001585155464/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001585155464 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 910) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/910 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/910' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCCc2cc(Br)ccc21) `ZINC001585155464.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585155464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001585155464/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001585155464 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCCc2cc(Br)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 1, 1, 1, 17, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 11, 11, 5, 1, 1, 1, 1, 3, 3, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 5, 5, 5, 11, 11, 5, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001585155464 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001585155464/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001585155464 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 911) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/911 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/911' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCCc2cc(Br)ccc21) `ZINC001585155464.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585155464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001585155464/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001585155464 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCCc2cc(Br)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 1, 1, 1, 17, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 11, 4, 1, 1, 1, 1, 4, 4, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4, 4, 4, 11, 11, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001585155464 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001585155464 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001585155464/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001585155464/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001585155464 Building ZINC001585155464 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001585155464' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001585155464 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001585155464 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001585155464/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001585155464 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 910) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCCc2cc(Br)ccc21) `ZINC001585155464.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001585155464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001585155464/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001585155464 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCCc2cc(Br)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 1, 1, 1, 17, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 11, 11, 5, 1, 1, 1, 1, 3, 3, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 5, 5, 5, 11, 11, 5, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001585155464 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001585155464/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001585155464 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 911) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCCc2cc(Br)ccc21) `ZINC001585155464.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001585155464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001585155464/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001585155464 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCCc2cc(Br)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 1, 1, 1, 17, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 11, 4, 1, 1, 1, 1, 4, 4, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4, 4, 4, 11, 11, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001585155464 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001585155464 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001585155464/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001585155464/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001585155464 Building ZINC001586200623 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586200623' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586200623 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586200623 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586200623/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586200623 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 912) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/912 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/912' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cccc(C[S@@](=O)C2CCCCC2)c1) `ZINC001586200623.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586200623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586200623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001586200623 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cccc(C[S@@](=O)C2CCCCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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.3', 'S.o', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 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, 8, 4, 1, 1, 1, 1, 3, 3, 3, 10, 10, 3, 10, 10, 16, 21, 27, 29, 29, 29, 29, 29, 10, 4, 4, 4, 4, 8, 8, 4, 3, 10, 10, 5, 16, 16, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 10] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 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: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586200623 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586200623/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586200623 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 913) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/913 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/913' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cccc(C[S@@](=O)C2CCCCC2)c1) `ZINC001586200623.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586200623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586200623/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001586200623 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cccc(C[S@@](=O)C2CCCCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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.3', 'S.o', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 conformations in 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, 7, 3, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 17, 20, 25, 27, 27, 27, 27, 27, 10, 3, 3, 3, 3, 7, 7, 3, 3, 10, 10, 10, 17, 17, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586200623 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001586200623 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586200623/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586200623/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586200623 Building ZINC001586200623 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586200623' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586200623 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586200623 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586200623/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586200623 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 912) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cccc(C[S@@](=O)C2CCCCC2)c1) `ZINC001586200623.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586200623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586200623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001586200623 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cccc(C[S@@](=O)C2CCCCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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.3', 'S.o', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 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, 8, 4, 1, 1, 1, 1, 3, 3, 3, 10, 10, 3, 10, 10, 16, 21, 27, 29, 29, 29, 29, 29, 10, 4, 4, 4, 4, 8, 8, 4, 3, 10, 10, 5, 16, 16, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 10] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 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: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586200623 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586200623/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586200623 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 913) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cccc(C[S@@](=O)C2CCCCC2)c1) `ZINC001586200623.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586200623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586200623/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001586200623 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cccc(C[S@@](=O)C2CCCCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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.3', 'S.o', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 conformations in 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, 7, 3, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 17, 20, 25, 27, 27, 27, 27, 27, 10, 3, 3, 3, 3, 7, 7, 3, 3, 10, 10, 10, 17, 17, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586200623 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001586200623 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586200623/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586200623/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586200623 Building ZINC001586200624 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586200624' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586200624 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586200624 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586200624/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586200624 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 914) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/914 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/914' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cccc(C[S@](=O)C2CCCCC2)c1) `ZINC001586200624.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586200624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586200624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001586200624 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cccc(C[S@](=O)C2CCCCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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.3', 'S.o', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 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, 8, 4, 1, 1, 1, 1, 3, 3, 3, 9, 9, 3, 9, 9, 16, 19, 23, 27, 27, 27, 27, 27, 9, 4, 4, 4, 4, 8, 8, 4, 3, 9, 9, 5, 16, 16, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 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]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586200624 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586200624/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586200624 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 915) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/915 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/915' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cccc(C[S@](=O)C2CCCCC2)c1) `ZINC001586200624.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586200624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586200624/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001586200624 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cccc(C[S@](=O)C2CCCCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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.3', 'S.o', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 conformations in 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, 7, 3, 1, 1, 1, 1, 3, 3, 3, 10, 10, 9, 10, 10, 16, 21, 27, 31, 31, 31, 31, 31, 10, 3, 3, 3, 3, 7, 7, 3, 3, 10, 10, 9, 16, 16, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 10] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 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: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586200624 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001586200624 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586200624/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586200624/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586200624 Building ZINC001586200624 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586200624' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586200624 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586200624 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586200624/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586200624 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 914) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/914: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cccc(C[S@](=O)C2CCCCC2)c1) `ZINC001586200624.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586200624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586200624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001586200624 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cccc(C[S@](=O)C2CCCCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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.3', 'S.o', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 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, 8, 4, 1, 1, 1, 1, 3, 3, 3, 9, 9, 3, 9, 9, 16, 19, 23, 27, 27, 27, 27, 27, 9, 4, 4, 4, 4, 8, 8, 4, 3, 9, 9, 5, 16, 16, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 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]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586200624 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586200624/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586200624 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 915) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/915: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cccc(C[S@](=O)C2CCCCC2)c1) `ZINC001586200624.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586200624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586200624/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001586200624 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cccc(C[S@](=O)C2CCCCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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.3', 'S.o', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 conformations in 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, 7, 3, 1, 1, 1, 1, 3, 3, 3, 10, 10, 9, 10, 10, 16, 21, 27, 31, 31, 31, 31, 31, 10, 3, 3, 3, 3, 7, 7, 3, 3, 10, 10, 9, 16, 16, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 10] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 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: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586200624 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001586200624 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586200624/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586200624/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586200624 Building ZINC001586283120 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586283120' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586283120 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586283120 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586283120/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586283120 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 916) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/916 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/916' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@]1(C(=O)OC(C)(C)C)CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CCO1) `ZINC001586283120.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586283120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586283120/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001586283120 none COC[C@]1(C(=O)OC(C)(C)C)CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 17, 6, 6, 6, 20, 20, 20, 20, 20, 20, 6, 4, 2, 4, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 6, 6, 6, 20, 20, 20, 17, 17, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 6, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586283120 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586283120/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586283120 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 917) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/917 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/917' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@]1(C(=O)OC(C)(C)C)CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CCO1) `ZINC001586283120.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586283120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586283120/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001586283120 none COC[C@]1(C(=O)OC(C)(C)C)CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 16, 16, 17, 17, 17, 17, 4, 4, 2, 4, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 4, 8, 8, 2, 2, 4, 4, 4, 13, 13, 13, 10, 10, 17, 17, 17, 17, 17, 17, 17, 17, 17, 4, 4, 2, 2, 2, 8, 8, 4, 8, 8, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 99 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586283120 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001586283120 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586283120/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586283120/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586283120 Building ZINC001586283120 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586283120' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586283120 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586283120 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586283120/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586283120 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 916) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COC[C@]1(C(=O)OC(C)(C)C)CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CCO1) `ZINC001586283120.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586283120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586283120/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001586283120 none COC[C@]1(C(=O)OC(C)(C)C)CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 17, 6, 6, 6, 20, 20, 20, 20, 20, 20, 6, 4, 2, 4, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 6, 6, 6, 20, 20, 20, 17, 17, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 6, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586283120 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586283120/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586283120 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 917) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COC[C@]1(C(=O)OC(C)(C)C)CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CCO1) `ZINC001586283120.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586283120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586283120/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001586283120 none COC[C@]1(C(=O)OC(C)(C)C)CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 16, 16, 17, 17, 17, 17, 4, 4, 2, 4, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 4, 8, 8, 2, 2, 4, 4, 4, 13, 13, 13, 10, 10, 17, 17, 17, 17, 17, 17, 17, 17, 17, 4, 4, 2, 2, 2, 8, 8, 4, 8, 8, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 99 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586283120 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001586283120 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586283120/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586283120/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586283120 Building ZINC001586283121 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586283121' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586283121 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586283121 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586283121/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586283121 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 918) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/918 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/918' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@]1(C(=O)OC(C)(C)C)CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CCO1) `ZINC001586283121.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586283121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586283121/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001586283121 none COC[C@@]1(C(=O)OC(C)(C)C)CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 9, 5, 5, 5, 16, 16, 17, 17, 17, 17, 5, 5, 2, 5, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 2, 2, 5, 5, 5, 12, 12, 12, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5, 2, 2, 2, 8, 8, 2, 8, 8, 2, 2, 2, 5, 5, 5, 5] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 86 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586283121 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586283121/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586283121 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 919) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/919 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/919' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@]1(C(=O)OC(C)(C)C)CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CCO1) `ZINC001586283121.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586283121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586283121/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001586283121 none COC[C@@]1(C(=O)OC(C)(C)C)CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 21, 21, 21, 21, 21, 21, 7, 5, 2, 5, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 7, 7, 7, 20, 20, 20, 18, 18, 21, 21, 21, 21, 21, 21, 21, 21, 21, 7, 7, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586283121 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001586283121 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586283121/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586283121/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586283121 Building ZINC001586283121 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586283121' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586283121 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586283121 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586283121/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586283121 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 918) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COC[C@@]1(C(=O)OC(C)(C)C)CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CCO1) `ZINC001586283121.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586283121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586283121/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001586283121 none COC[C@@]1(C(=O)OC(C)(C)C)CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 9, 5, 5, 5, 16, 16, 17, 17, 17, 17, 5, 5, 2, 5, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 2, 2, 5, 5, 5, 12, 12, 12, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5, 2, 2, 2, 8, 8, 2, 8, 8, 2, 2, 2, 5, 5, 5, 5] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 86 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586283121 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586283121/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586283121 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 919) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COC[C@@]1(C(=O)OC(C)(C)C)CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CCO1) `ZINC001586283121.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586283121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586283121/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001586283121 none COC[C@@]1(C(=O)OC(C)(C)C)CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 21, 21, 21, 21, 21, 21, 7, 5, 2, 5, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 7, 7, 7, 20, 20, 20, 18, 18, 21, 21, 21, 21, 21, 21, 21, 21, 21, 7, 7, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586283121 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001586283121 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586283121/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586283121/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586283121 Building ZINC001586684302 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586684302' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586684302 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586684302 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586684302/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586684302 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 920) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/920 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/920' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCN1CCOCC1)C1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001586684302.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586684302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586684302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001586684302 none O=C(NCCCN1CCOCC1)C1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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: [11, 1, 8, 5, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 7, 7, 24, 29, 41, 50, 50, 50, 50, 50, 4, 4, 4, 2, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 24, 24, 32, 32, 39, 40, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [51, 50, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 53, 54, 55, 56]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586684302 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586684302/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586684302 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 921) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/921 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/921' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCN1CCOCC1)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001586684302.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586684302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586684302/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001586684302 none O=C(NCCCN1CCOCC1)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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: [11, 1, 8, 5, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 8, 24, 28, 37, 50, 50, 50, 50, 50, 4, 4, 4, 2, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 24, 24, 30, 30, 36, 37, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [51, 50, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 53, 54, 55, 56]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586684302 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001586684302 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586684302/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586684302/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586684302 Building ZINC001586684302 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586684302' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586684302 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586684302 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586684302/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586684302 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 920) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: O=C(NCCCN1CCOCC1)C1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001586684302.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586684302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586684302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001586684302 none O=C(NCCCN1CCOCC1)C1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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: [11, 1, 8, 5, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 7, 7, 24, 29, 41, 50, 50, 50, 50, 50, 4, 4, 4, 2, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 24, 24, 32, 32, 39, 40, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [51, 50, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 53, 54, 55, 56]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586684302 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586684302/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586684302 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 921) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: O=C(NCCCN1CCOCC1)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001586684302.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586684302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586684302/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001586684302 none O=C(NCCCN1CCOCC1)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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: [11, 1, 8, 5, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 8, 24, 28, 37, 50, 50, 50, 50, 50, 4, 4, 4, 2, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 24, 24, 30, 30, 36, 37, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [51, 50, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 53, 54, 55, 56]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586684302 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001586684302 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586684302/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586684302/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586684302 Building ZINC001586900758 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900758' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900758 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586900758 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900758/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900758 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 922) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/922 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/922' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)C(F)(F)F)[C@@H]1C(=O)OC(C)(C)C) `ZINC001586900758.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586900758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001586900758 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)C(F)(F)F)[C@@H]1C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 15, 15, 15, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 8, 8, 8, 8, 8, 8, 20, 20, 20, 20, 20, 20, 8, 8, 8, 30, 30, 35, 36, 36, 36, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 20, 36, 36, 36, 36, 36, 36, 36, 36, 36] 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]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900758 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900758/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900758 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 923) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/923 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/923' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)C(F)(F)F)[C@@H]1C(=O)OC(C)(C)C) `ZINC001586900758.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586900758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900758/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001586900758 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)C(F)(F)F)[C@@H]1C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 15, 15, 15, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 7, 7, 7, 7, 7, 7, 19, 19, 19, 19, 19, 19, 7, 7, 7, 26, 26, 31, 31, 31, 31, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 19, 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, 51, 52, 53, 54, 55, 56]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900758 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001586900758 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900758/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900758/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900758 Building ZINC001586900758 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900758' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900758 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586900758 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900758/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900758 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 922) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)C(F)(F)F)[C@@H]1C(=O)OC(C)(C)C) `ZINC001586900758.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586900758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001586900758 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)C(F)(F)F)[C@@H]1C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 15, 15, 15, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 8, 8, 8, 8, 8, 8, 20, 20, 20, 20, 20, 20, 8, 8, 8, 30, 30, 35, 36, 36, 36, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 20, 36, 36, 36, 36, 36, 36, 36, 36, 36] 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]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900758 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900758/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900758 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 923) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)C(F)(F)F)[C@@H]1C(=O)OC(C)(C)C) `ZINC001586900758.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586900758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900758/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001586900758 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)C(F)(F)F)[C@@H]1C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 15, 15, 15, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 7, 7, 7, 7, 7, 7, 19, 19, 19, 19, 19, 19, 7, 7, 7, 26, 26, 31, 31, 31, 31, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 19, 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, 51, 52, 53, 54, 55, 56]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900758 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001586900758 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900758/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900758/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900758 Building ZINC001586900759 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900759' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900759 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586900759 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900759/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900759 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 924) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/924 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/924' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](NC(=O)C(F)(F)F)[C@H]1C(=O)OC(C)(C)C) `ZINC001586900759.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586900759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900759/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001586900759 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](NC(=O)C(F)(F)F)[C@H]1C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 15, 15, 15, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 11, 11, 11, 11, 11, 11, 5, 5, 5, 23, 23, 35, 36, 36, 36, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 11, 36, 36, 36, 36, 36, 36, 36, 36, 36] 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]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900759 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900759/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900759 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 925) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/925 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/925' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](NC(=O)C(F)(F)F)[C@H]1C(=O)OC(C)(C)C) `ZINC001586900759.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586900759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900759/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001586900759 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](NC(=O)C(F)(F)F)[C@H]1C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 15, 15, 15, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 5, 5, 7, 7, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18, 7, 7, 7, 30, 30, 35, 35, 35, 35, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 18, 35, 35, 35, 35, 35, 35, 35, 35, 35] 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]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900759 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001586900759 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900759/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900759/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900759 Building ZINC001586900759 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900759' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900759 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586900759 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900759/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900759 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 924) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](NC(=O)C(F)(F)F)[C@H]1C(=O)OC(C)(C)C) `ZINC001586900759.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586900759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900759/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001586900759 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](NC(=O)C(F)(F)F)[C@H]1C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 15, 15, 15, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 11, 11, 11, 11, 11, 11, 5, 5, 5, 23, 23, 35, 36, 36, 36, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 11, 36, 36, 36, 36, 36, 36, 36, 36, 36] 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]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900759 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900759/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900759 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 925) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](NC(=O)C(F)(F)F)[C@H]1C(=O)OC(C)(C)C) `ZINC001586900759.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586900759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900759/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001586900759 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](NC(=O)C(F)(F)F)[C@H]1C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 15, 15, 15, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 5, 5, 7, 7, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18, 7, 7, 7, 30, 30, 35, 35, 35, 35, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 18, 35, 35, 35, 35, 35, 35, 35, 35, 35] 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]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900759 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001586900759 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900759/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900759/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900759 Building ZINC001586900760 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900760' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586900760 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900760/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 926) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/926 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/926' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](NC(=O)C(F)(F)F)[C@@H]1C(=O)OC(C)(C)C) `ZINC001586900760.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586900760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001586900760 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](NC(=O)C(F)(F)F)[C@@H]1C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 15, 15, 15, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 2, 5, 6, 10, 10, 10, 10, 10, 10, 20, 20, 20, 20, 20, 20, 10, 10, 10, 29, 29, 33, 33, 33, 33, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 20, 33, 33, 33, 33, 33, 33, 33, 33, 33] 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, 55, 56]) total number of confs: 127 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900760/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 927) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/927 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/927' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](NC(=O)C(F)(F)F)[C@@H]1C(=O)OC(C)(C)C) `ZINC001586900760.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586900760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900760/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001586900760 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](NC(=O)C(F)(F)F)[C@@H]1C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 15, 15, 15, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 5, 5, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 6, 6, 6, 20, 20, 29, 30, 30, 30, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 9, 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, 51, 52, 53, 54, 55, 56]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001586900760 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900760/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900760/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900760 Building ZINC001586900760 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900760' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586900760 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900760/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 926) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](NC(=O)C(F)(F)F)[C@@H]1C(=O)OC(C)(C)C) `ZINC001586900760.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586900760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001586900760 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](NC(=O)C(F)(F)F)[C@@H]1C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 15, 15, 15, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 2, 5, 6, 10, 10, 10, 10, 10, 10, 20, 20, 20, 20, 20, 20, 10, 10, 10, 29, 29, 33, 33, 33, 33, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 20, 33, 33, 33, 33, 33, 33, 33, 33, 33] 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, 55, 56]) total number of confs: 127 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900760/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 927) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](NC(=O)C(F)(F)F)[C@@H]1C(=O)OC(C)(C)C) `ZINC001586900760.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586900760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900760/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001586900760 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](NC(=O)C(F)(F)F)[C@@H]1C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 15, 15, 15, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 5, 5, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 6, 6, 6, 20, 20, 29, 30, 30, 30, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 9, 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, 51, 52, 53, 54, 55, 56]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001586900760 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900760/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900760/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900760 Building ZINC001586900761 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900761' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900761 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586900761 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900761/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900761 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 928) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/928 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/928' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)C(F)(F)F)[C@H]1C(=O)OC(C)(C)C) `ZINC001586900761.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586900761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001586900761 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)C(F)(F)F)[C@H]1C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 15, 15, 15, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 5, 5, 6, 6, 6, 6, 6, 6, 10, 10, 10, 10, 10, 10, 6, 6, 6, 19, 19, 28, 28, 28, 28, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 10, 28, 28, 28, 28, 28, 28, 28, 28, 28] 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900761 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900761/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900761 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 929) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/929 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/929' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)C(F)(F)F)[C@H]1C(=O)OC(C)(C)C) `ZINC001586900761.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586900761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900761/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001586900761 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)C(F)(F)F)[C@H]1C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 15, 15, 15, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 2, 5, 6, 10, 10, 10, 10, 10, 10, 20, 20, 20, 20, 20, 20, 10, 10, 10, 28, 28, 32, 32, 32, 32, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 20, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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, 55, 56]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900761 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001586900761 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900761/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900761/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900761 Building ZINC001586900761 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900761' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900761 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586900761 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900761/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900761 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 928) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)C(F)(F)F)[C@H]1C(=O)OC(C)(C)C) `ZINC001586900761.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586900761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001586900761 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)C(F)(F)F)[C@H]1C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 15, 15, 15, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 5, 5, 6, 6, 6, 6, 6, 6, 10, 10, 10, 10, 10, 10, 6, 6, 6, 19, 19, 28, 28, 28, 28, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 10, 28, 28, 28, 28, 28, 28, 28, 28, 28] 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900761 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900761/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900761 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 929) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)C(F)(F)F)[C@H]1C(=O)OC(C)(C)C) `ZINC001586900761.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586900761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900761/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001586900761 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](NC(=O)C(F)(F)F)[C@H]1C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 15, 15, 15, 5, 7, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 2, 5, 6, 10, 10, 10, 10, 10, 10, 20, 20, 20, 20, 20, 20, 10, 10, 10, 28, 28, 32, 32, 32, 32, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 20, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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, 55, 56]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900761 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001586900761 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900761/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900761/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586900761 Building ZINC001586926988 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586926988' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586926988 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586926988 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586926988/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586926988 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 930) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/930 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/930' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NCCNS(=O)(=O)c1cc(C)ccc1Br) `ZINC001586926988.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586926988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586926988/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001586926988 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NCCNS(=O)(=O)c1cc(C)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 5, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 6, 6, 6, 10, 12, 22, 42, 42, 42, 45, 45, 45, 44, 45, 45, 45, 4, 4, 4, 4, 4, 4, 4, 6, 10, 10, 12, 12, 22, 45, 45, 45, 45, 44, 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]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586926988 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586926988/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586926988 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 931) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/931 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/931' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCCNS(=O)(=O)c1cc(C)ccc1Br) `ZINC001586926988.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586926988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586926988/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001586926988 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCCNS(=O)(=O)c1cc(C)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 5, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 6, 6, 6, 10, 12, 23, 42, 42, 42, 45, 45, 45, 45, 45, 45, 45, 4, 4, 4, 4, 4, 4, 4, 6, 10, 10, 12, 12, 23, 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]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586926988 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001586926988 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586926988/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586926988/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586926988 Building ZINC001586926988 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586926988' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586926988 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001586926988 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586926988/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586926988 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 930) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)NCCNS(=O)(=O)c1cc(C)ccc1Br) `ZINC001586926988.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001586926988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586926988/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001586926988 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NCCNS(=O)(=O)c1cc(C)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 5, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 6, 6, 6, 10, 12, 22, 42, 42, 42, 45, 45, 45, 44, 45, 45, 45, 4, 4, 4, 4, 4, 4, 4, 6, 10, 10, 12, 12, 22, 45, 45, 45, 45, 44, 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]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586926988 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586926988/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586926988 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 931) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCCNS(=O)(=O)c1cc(C)ccc1Br) `ZINC001586926988.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001586926988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586926988/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001586926988 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCCNS(=O)(=O)c1cc(C)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 1, 1, 1, 5, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 6, 6, 6, 10, 12, 23, 42, 42, 42, 45, 45, 45, 45, 45, 45, 45, 4, 4, 4, 4, 4, 4, 4, 6, 10, 10, 12, 12, 23, 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]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586926988 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001586926988 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586926988/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586926988/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001586926988 Building ZINC001587433785 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001587433785' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001587433785 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587433785 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001587433785/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001587433785 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 932) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/932 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/932' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCNS(=O)(=O)c1cccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1) `ZINC001587433785.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587433785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001587433785/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001587433785 none COCCNS(=O)(=O)c1cccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 34, 32, 12, 8, 6, 8, 8, 6, 2, 6, 6, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 6, 35, 35, 35, 34, 34, 32, 32, 12, 2, 6, 6, 2, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 4, 6] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001587433785 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001587433785/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001587433785 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 933) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/933 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/933' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCNS(=O)(=O)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1) `ZINC001587433785.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587433785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001587433785/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001587433785 none COCCNS(=O)(=O)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 41, 39, 14, 8, 6, 8, 8, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 6, 42, 42, 42, 41, 41, 39, 39, 14, 6, 6, 6, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 6] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001587433785 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001587433785 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001587433785/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001587433785/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001587433785 Building ZINC001587433785 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001587433785' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001587433785 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001587433785 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001587433785/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001587433785 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 932) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COCCNS(=O)(=O)c1cccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1) `ZINC001587433785.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001587433785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001587433785/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001587433785 none COCCNS(=O)(=O)c1cccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 34, 32, 12, 8, 6, 8, 8, 6, 2, 6, 6, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 6, 35, 35, 35, 34, 34, 32, 32, 12, 2, 6, 6, 2, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 4, 6] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001587433785 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001587433785/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001587433785 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 933) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COCCNS(=O)(=O)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1) `ZINC001587433785.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001587433785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001587433785/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001587433785 none COCCNS(=O)(=O)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', '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.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 41, 39, 14, 8, 6, 8, 8, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 6, 42, 42, 42, 41, 41, 39, 39, 14, 6, 6, 6, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 6] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001587433785 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001587433785 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001587433785/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001587433785/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001587433785 Building ZINC001588212091 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001588212091' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001588212091 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001588212091 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001588212091/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001588212091 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 934) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/934 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/934' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(S(=O)(=O)c2ccccc2Cl)CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001588212091.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001588212091.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001588212091/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001588212091 none O=C(N1CCN(S(=O)(=O)c2ccccc2Cl)CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 16, 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, 6, 6, 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: [2, 1, 4, 9, 9, 9, 9, 19, 19, 19, 31, 31, 31, 31, 31, 31, 9, 9, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 31, 31, 31, 31, 9, 9, 9, 9, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001588212091 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001588212091/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001588212091 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 935) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/935 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/935' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(S(=O)(=O)c2ccccc2Cl)CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001588212091.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001588212091.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001588212091/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001588212091 none O=C(N1CCN(S(=O)(=O)c2ccccc2Cl)CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 16, 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, 6, 6, 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, 5, 10, 10, 10, 10, 19, 19, 19, 30, 30, 30, 30, 30, 30, 10, 10, 1, 1, 1, 4, 4, 4, 4, 6, 6, 4, 6, 6, 4, 10, 10, 10, 10, 30, 30, 30, 30, 10, 10, 10, 10, 4, 6, 6, 4, 6, 6, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001588212091 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001588212091 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001588212091/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001588212091/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001588212091 Building ZINC001588212091 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001588212091' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001588212091 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001588212091 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001588212091/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001588212091 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 934) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: O=C(N1CCN(S(=O)(=O)c2ccccc2Cl)CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001588212091.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001588212091.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001588212091/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001588212091 none O=C(N1CCN(S(=O)(=O)c2ccccc2Cl)CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 16, 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, 6, 6, 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: [2, 1, 4, 9, 9, 9, 9, 19, 19, 19, 31, 31, 31, 31, 31, 31, 9, 9, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 31, 31, 31, 31, 9, 9, 9, 9, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001588212091 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001588212091/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001588212091 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 935) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: O=C(N1CCN(S(=O)(=O)c2ccccc2Cl)CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001588212091.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001588212091.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001588212091/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001588212091 none O=C(N1CCN(S(=O)(=O)c2ccccc2Cl)CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 16, 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, 6, 6, 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, 5, 10, 10, 10, 10, 19, 19, 19, 30, 30, 30, 30, 30, 30, 10, 10, 1, 1, 1, 4, 4, 4, 4, 6, 6, 4, 6, 6, 4, 10, 10, 10, 10, 30, 30, 30, 30, 10, 10, 10, 10, 4, 6, 6, 4, 6, 6, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001588212091 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001588212091 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001588212091/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001588212091/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001588212091 Building ZINC001596358087 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358087' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358087 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001596358087 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358087/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358087 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 936) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/936 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/936' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@H]1C(=O)NC[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC001596358087.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001596358087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 69 natoms 68 natoms 67 natoms 66 names: ZINC001596358087 none CC(C)(C)OC(=O)N1CCC[C@H]1C(=O)NC[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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', '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, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 48, 34, 48, 34, 34, 34, 34, 23, 34, 23, 23, 12, 4, 4, 4, 4, 4, 4, 2, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 34, 34, 23, 12, 12, 4, 4, 4, 4, 4, 4, 1, 1, 2, 1, 1, 4, 4] 100 rigid atoms, others: [32, 33, 59, 60, 63, 62, 23, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 61, 64, 65]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358087 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358087/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358087 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 937) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/937 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/937' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@H]1C(=O)NC[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC001596358087.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001596358087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358087/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 69 natoms 68 natoms 67 natoms 66 names: ZINC001596358087 none CC(C)(C)OC(=O)N1CCC[C@H]1C(=O)NC[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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', '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, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 39, 24, 39, 24, 24, 24, 24, 20, 24, 20, 20, 13, 4, 4, 4, 4, 4, 4, 2, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 24, 24, 20, 13, 13, 4, 4, 4, 4, 4, 4, 1, 1, 2, 1, 1, 4, 4] 100 rigid atoms, others: [32, 33, 59, 60, 63, 62, 23, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 61, 64, 65]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358087 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001596358087 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358087/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358087/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358087 Building ZINC001596358087 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358087' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358087 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001596358087 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358087/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358087 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 936) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/936: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@H]1C(=O)NC[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC001596358087.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001596358087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 69 natoms 68 natoms 67 natoms 66 names: ZINC001596358087 none CC(C)(C)OC(=O)N1CCC[C@H]1C(=O)NC[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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', '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, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 48, 34, 48, 34, 34, 34, 34, 23, 34, 23, 23, 12, 4, 4, 4, 4, 4, 4, 2, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 34, 34, 23, 12, 12, 4, 4, 4, 4, 4, 4, 1, 1, 2, 1, 1, 4, 4] 100 rigid atoms, others: [32, 33, 59, 60, 63, 62, 23, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 61, 64, 65]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358087 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358087/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358087 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 937) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/937: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@H]1C(=O)NC[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC001596358087.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001596358087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358087/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 69 natoms 68 natoms 67 natoms 66 names: ZINC001596358087 none CC(C)(C)OC(=O)N1CCC[C@H]1C(=O)NC[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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', '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, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 39, 24, 39, 24, 24, 24, 24, 20, 24, 20, 20, 13, 4, 4, 4, 4, 4, 4, 2, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 24, 24, 20, 13, 13, 4, 4, 4, 4, 4, 4, 1, 1, 2, 1, 1, 4, 4] 100 rigid atoms, others: [32, 33, 59, 60, 63, 62, 23, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 61, 64, 65]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358087 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001596358087 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358087/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358087/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358087 Building ZINC001596358088 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358088' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358088 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001596358088 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358088/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358088 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 938) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/938 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/938' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@H]1C(=O)NC[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC001596358088.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001596358088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358088/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 69 natoms 68 natoms 67 natoms 66 names: ZINC001596358088 none CC(C)(C)OC(=O)N1CCC[C@H]1C(=O)NC[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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', '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, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 44, 31, 44, 31, 31, 31, 31, 27, 31, 23, 23, 9, 3, 3, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 23, 9, 9, 3, 3, 3, 3, 3, 3, 2, 2, 4, 2, 2, 3, 3] 100 rigid atoms, others: [23, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 173 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358088 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358088/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358088 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 939) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/939 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/939' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@H]1C(=O)NC[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC001596358088.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001596358088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358088/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 69 natoms 68 natoms 67 natoms 66 names: ZINC001596358088 none CC(C)(C)OC(=O)N1CCC[C@H]1C(=O)NC[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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', '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, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 38, 24, 38, 24, 24, 24, 24, 21, 24, 18, 18, 9, 3, 3, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 24, 24, 18, 9, 9, 3, 3, 3, 3, 3, 3, 2, 2, 4, 2, 2, 3, 3] 100 rigid atoms, others: [23, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358088 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001596358088 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358088/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358088/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358088 Building ZINC001596358088 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358088' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358088 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001596358088 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358088/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358088 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 938) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/938: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@H]1C(=O)NC[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC001596358088.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001596358088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358088/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 69 natoms 68 natoms 67 natoms 66 names: ZINC001596358088 none CC(C)(C)OC(=O)N1CCC[C@H]1C(=O)NC[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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', '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, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 44, 31, 44, 31, 31, 31, 31, 27, 31, 23, 23, 9, 3, 3, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 23, 9, 9, 3, 3, 3, 3, 3, 3, 2, 2, 4, 2, 2, 3, 3] 100 rigid atoms, others: [23, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 173 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358088 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358088/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358088 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 939) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/939: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@H]1C(=O)NC[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC001596358088.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001596358088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358088/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 69 natoms 68 natoms 67 natoms 66 names: ZINC001596358088 none CC(C)(C)OC(=O)N1CCC[C@H]1C(=O)NC[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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', '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, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 38, 24, 38, 24, 24, 24, 24, 21, 24, 18, 18, 9, 3, 3, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 24, 24, 18, 9, 9, 3, 3, 3, 3, 3, 3, 2, 2, 4, 2, 2, 3, 3] 100 rigid atoms, others: [23, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358088 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001596358088 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358088/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358088/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358088 Building ZINC001596358089 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358089' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358089 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001596358089 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358089/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358089 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 940) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/940 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/940' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@@H]1C(=O)NC[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC001596358089.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001596358089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358089/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 69 natoms 68 natoms 67 natoms 66 names: ZINC001596358089 none CC(C)(C)OC(=O)N1CCC[C@@H]1C(=O)NC[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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', '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, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 41, 26, 41, 26, 26, 26, 26, 21, 26, 21, 21, 13, 4, 4, 4, 4, 4, 4, 2, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 26, 26, 26, 21, 13, 13, 4, 4, 4, 4, 4, 4, 1, 1, 2, 1, 1, 4, 4] 100 rigid atoms, others: [32, 33, 59, 60, 63, 62, 23, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 61, 64, 65]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358089 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358089/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358089 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 941) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/941 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/941' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@@H]1C(=O)NC[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC001596358089.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001596358089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358089/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 69 natoms 68 natoms 67 natoms 66 names: ZINC001596358089 none CC(C)(C)OC(=O)N1CCC[C@@H]1C(=O)NC[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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', '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, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 42, 28, 42, 28, 28, 28, 28, 19, 28, 19, 19, 9, 3, 3, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28, 28, 28, 19, 9, 9, 3, 3, 3, 3, 3, 3, 1, 1, 2, 1, 1, 3, 3] 100 rigid atoms, others: [32, 33, 59, 60, 63, 62, 23, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 61, 64, 65]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358089 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001596358089 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358089/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358089/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358089 Building ZINC001596358089 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358089' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358089 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001596358089 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358089/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358089 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 940) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/940: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@@H]1C(=O)NC[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC001596358089.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001596358089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358089/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 69 natoms 68 natoms 67 natoms 66 names: ZINC001596358089 none CC(C)(C)OC(=O)N1CCC[C@@H]1C(=O)NC[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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', '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, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 41, 26, 41, 26, 26, 26, 26, 21, 26, 21, 21, 13, 4, 4, 4, 4, 4, 4, 2, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 26, 26, 26, 21, 13, 13, 4, 4, 4, 4, 4, 4, 1, 1, 2, 1, 1, 4, 4] 100 rigid atoms, others: [32, 33, 59, 60, 63, 62, 23, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 61, 64, 65]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358089 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358089/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358089 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 941) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/941: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@@H]1C(=O)NC[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC001596358089.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001596358089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358089/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 69 natoms 68 natoms 67 natoms 66 names: ZINC001596358089 none CC(C)(C)OC(=O)N1CCC[C@@H]1C(=O)NC[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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', '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, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 42, 28, 42, 28, 28, 28, 28, 19, 28, 19, 19, 9, 3, 3, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28, 28, 28, 19, 9, 9, 3, 3, 3, 3, 3, 3, 1, 1, 2, 1, 1, 3, 3] 100 rigid atoms, others: [32, 33, 59, 60, 63, 62, 23, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 61, 64, 65]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358089 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001596358089 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358089/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358089/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358089 Building ZINC001596358090 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358090' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358090 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001596358090 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358090/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358090 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 942) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/942 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/942' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@@H]1C(=O)NC[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC001596358090.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001596358090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358090/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 69 natoms 68 natoms 67 natoms 66 names: ZINC001596358090 none CC(C)(C)OC(=O)N1CCC[C@@H]1C(=O)NC[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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', '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, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 34, 50, 34, 34, 34, 34, 27, 34, 27, 27, 11, 4, 4, 4, 4, 4, 4, 2, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 34, 34, 27, 11, 11, 4, 4, 4, 4, 4, 4, 2, 2, 4, 2, 2, 4, 4] 100 rigid atoms, others: [23, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358090 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358090/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358090 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 943) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/943 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/943' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@@H]1C(=O)NC[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC001596358090.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001596358090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358090/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 69 natoms 68 natoms 67 natoms 66 names: ZINC001596358090 none CC(C)(C)OC(=O)N1CCC[C@@H]1C(=O)NC[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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', '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, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 41, 24, 41, 24, 24, 24, 24, 21, 24, 20, 20, 8, 3, 3, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 24, 24, 20, 8, 8, 3, 3, 3, 3, 3, 3, 2, 2, 4, 2, 2, 3, 3] 100 rigid atoms, others: [23, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358090 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001596358090 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358090/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358090/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358090 Building ZINC001596358090 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358090' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358090 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001596358090 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358090/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358090 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 942) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC(C)(C)OC(=O)N1CCC[C@@H]1C(=O)NC[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC001596358090.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001596358090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358090/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 69 natoms 68 natoms 67 natoms 66 names: ZINC001596358090 none CC(C)(C)OC(=O)N1CCC[C@@H]1C(=O)NC[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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', '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, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 34, 50, 34, 34, 34, 34, 27, 34, 27, 27, 11, 4, 4, 4, 4, 4, 4, 2, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 34, 34, 27, 11, 11, 4, 4, 4, 4, 4, 4, 2, 2, 4, 2, 2, 4, 4] 100 rigid atoms, others: [23, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358090 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358090/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358090 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 943) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CC(C)(C)OC(=O)N1CCC[C@@H]1C(=O)NC[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC001596358090.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001596358090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358090/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 69 natoms 68 natoms 67 natoms 66 names: ZINC001596358090 none CC(C)(C)OC(=O)N1CCC[C@@H]1C(=O)NC[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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', '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, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 41, 24, 41, 24, 24, 24, 24, 21, 24, 20, 20, 8, 3, 3, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 24, 24, 20, 8, 8, 3, 3, 3, 3, 3, 3, 2, 2, 4, 2, 2, 3, 3] 100 rigid atoms, others: [23, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358090 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001596358090 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358090/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358090/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596358090 Building ZINC001596495516 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596495516' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596495516 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001596495516 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596495516/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596495516 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 944) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/944 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/944' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCCCc1cc(c2ccccc2)n[nH]1)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001596495516.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001596495516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596495516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001596495516 none CN(CCCCCc1cc(c2ccccc2)n[nH]1)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', '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.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 6, 7, 7, 7, 7, 18, 18, 18, 25, 25, 21, 25, 25, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 2, 2, 2, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 18, 25, 25, 21, 25, 25, 1, 4, 4, 1, 1, 1, 1] 50 rigid atoms, others: [32, 1, 57, 55, 56, 19, 20, 21, 22, 23, 24, 25, 26, 52, 58, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 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/418326/xbt-8058088.46/working/building/ZINC001596495516 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596495516/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596495516 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 945) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/945 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/945' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCCCc1cc(c2ccccc2)n[nH]1)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001596495516.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001596495516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596495516/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001596495516 none CN(CCCCCc1cc(c2ccccc2)n[nH]1)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', '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.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 6, 7, 7, 7, 7, 18, 18, 18, 22, 22, 20, 22, 22, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 2, 2, 2, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 18, 22, 22, 20, 22, 22, 1, 4, 4, 1, 1, 1, 1] 50 rigid atoms, others: [32, 1, 57, 55, 56, 19, 20, 21, 22, 23, 24, 25, 26, 52, 58, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 53, 54]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596495516 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001596495516 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596495516/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596495516/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596495516 Building ZINC001596495516 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596495516' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596495516 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001596495516 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596495516/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596495516 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 944) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CN(CCCCCc1cc(c2ccccc2)n[nH]1)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001596495516.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001596495516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596495516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001596495516 none CN(CCCCCc1cc(c2ccccc2)n[nH]1)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', '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.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 6, 7, 7, 7, 7, 18, 18, 18, 25, 25, 21, 25, 25, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 2, 2, 2, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 18, 25, 25, 21, 25, 25, 1, 4, 4, 1, 1, 1, 1] 50 rigid atoms, others: [32, 1, 57, 55, 56, 19, 20, 21, 22, 23, 24, 25, 26, 52, 58, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 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/418326/xbt-8058088.46/working/building/ZINC001596495516 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596495516/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596495516 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 945) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CN(CCCCCc1cc(c2ccccc2)n[nH]1)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001596495516.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001596495516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596495516/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001596495516 none CN(CCCCCc1cc(c2ccccc2)n[nH]1)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', '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.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 6, 7, 7, 7, 7, 18, 18, 18, 22, 22, 20, 22, 22, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 2, 2, 2, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 18, 22, 22, 20, 22, 22, 1, 4, 4, 1, 1, 1, 1] 50 rigid atoms, others: [32, 1, 57, 55, 56, 19, 20, 21, 22, 23, 24, 25, 26, 52, 58, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 53, 54]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596495516 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001596495516 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596495516/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596495516/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001596495516 Building ZINC001597039940 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597039940' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597039940 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001597039940 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597039940/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597039940 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 946) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/946 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/946' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](C(=O)N2CCN(C(=O)OC(C)(C)C)CC2)C1) `ZINC001597039940.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001597039940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597039940/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001597039940 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](C(=O)N2CCN(C(=O)OC(C)(C)C)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 3, 4, 4, 4, 4, 4, 7, 15, 25, 27, 27, 27, 27, 36, 36, 48, 48, 48, 48, 27, 27, 4, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 48, 48, 48, 48, 48, 48, 48, 48, 48, 27, 27, 27, 27, 4, 4] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 119 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597039940 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597039940/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597039940 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 947) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/947 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/947' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](C(=O)N2CCN(C(=O)OC(C)(C)C)CC2)C1) `ZINC001597039940.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001597039940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597039940/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001597039940 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](C(=O)N2CCN(C(=O)OC(C)(C)C)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 2, 4, 6, 8, 8, 8, 8, 8, 12, 22, 27, 30, 30, 30, 30, 38, 38, 49, 49, 49, 49, 30, 30, 8, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 30, 30, 30, 30, 49, 49, 49, 49, 49, 49, 49, 49, 49, 30, 30, 30, 30, 8, 8] 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, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 123 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597039940 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001597039940 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597039940/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597039940/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597039940 Building ZINC001597039940 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597039940' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597039940 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001597039940 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597039940/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597039940 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 946) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](C(=O)N2CCN(C(=O)OC(C)(C)C)CC2)C1) `ZINC001597039940.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001597039940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597039940/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001597039940 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](C(=O)N2CCN(C(=O)OC(C)(C)C)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 3, 4, 4, 4, 4, 4, 7, 15, 25, 27, 27, 27, 27, 36, 36, 48, 48, 48, 48, 27, 27, 4, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 48, 48, 48, 48, 48, 48, 48, 48, 48, 27, 27, 27, 27, 4, 4] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 119 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597039940 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597039940/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597039940 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 947) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](C(=O)N2CCN(C(=O)OC(C)(C)C)CC2)C1) `ZINC001597039940.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001597039940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597039940/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001597039940 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](C(=O)N2CCN(C(=O)OC(C)(C)C)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 2, 4, 6, 8, 8, 8, 8, 8, 12, 22, 27, 30, 30, 30, 30, 38, 38, 49, 49, 49, 49, 30, 30, 8, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 30, 30, 30, 30, 49, 49, 49, 49, 49, 49, 49, 49, 49, 30, 30, 30, 30, 8, 8] 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, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 123 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597039940 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001597039940 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597039940/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597039940/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597039940 Building ZINC001597039941 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597039941' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597039941 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001597039941 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597039941/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597039941 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 948) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/948 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/948' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(=O)N2CCN(C(=O)OC(C)(C)C)CC2)C1) `ZINC001597039941.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001597039941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597039941/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001597039941 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(=O)N2CCN(C(=O)OC(C)(C)C)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 7, 7, 7, 7, 7, 12, 19, 33, 37, 37, 37, 37, 41, 41, 48, 48, 48, 48, 37, 37, 7, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 37, 37, 37, 37, 48, 48, 48, 48, 48, 48, 48, 48, 48, 37, 37, 37, 37, 7, 7] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 110 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597039941 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597039941/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597039941 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 949) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/949 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/949' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(=O)N2CCN(C(=O)OC(C)(C)C)CC2)C1) `ZINC001597039941.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001597039941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597039941/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001597039941 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(=O)N2CCN(C(=O)OC(C)(C)C)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 2, 3, 3, 4, 4, 4, 4, 4, 7, 12, 22, 30, 30, 30, 30, 38, 38, 49, 49, 49, 49, 30, 30, 4, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 49, 49, 49, 49, 49, 49, 49, 49, 49, 30, 30, 30, 30, 4, 4] 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, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 112 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597039941 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001597039941 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597039941/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597039941/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597039941 Building ZINC001597039941 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597039941' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597039941 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001597039941 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597039941/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597039941 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 948) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(=O)N2CCN(C(=O)OC(C)(C)C)CC2)C1) `ZINC001597039941.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001597039941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597039941/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001597039941 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(=O)N2CCN(C(=O)OC(C)(C)C)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 7, 7, 7, 7, 7, 12, 19, 33, 37, 37, 37, 37, 41, 41, 48, 48, 48, 48, 37, 37, 7, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 37, 37, 37, 37, 48, 48, 48, 48, 48, 48, 48, 48, 48, 37, 37, 37, 37, 7, 7] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 110 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597039941 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597039941/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597039941 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 949) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(=O)N2CCN(C(=O)OC(C)(C)C)CC2)C1) `ZINC001597039941.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001597039941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597039941/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001597039941 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(=O)N2CCN(C(=O)OC(C)(C)C)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 2, 3, 3, 4, 4, 4, 4, 4, 7, 12, 22, 30, 30, 30, 30, 38, 38, 49, 49, 49, 49, 30, 30, 4, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 49, 49, 49, 49, 49, 49, 49, 49, 49, 30, 30, 30, 30, 4, 4] 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, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 112 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597039941 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001597039941 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597039941/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597039941/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597039941 Building ZINC001597371034 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597371034' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597371034 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001597371034 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597371034/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597371034 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 950) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/950 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/950' -> `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)Nc1cc(S(=O)(=O)NC2CC2)ccc1O) `ZINC001597371034.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001597371034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597371034/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001597371034 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(S(=O)(=O)NC2CC2)ccc1O NO_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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 14, 11, 11, 8, 5, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] 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, 6, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 5, 7, 7, 3, 3, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 10, 10, 10, 19, 34, 34, 7, 7, 7, 7, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 3, 7, 19, 34, 34, 34, 34, 34, 7, 7, 14] 100 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: 150 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597371034 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597371034/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597371034 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 951) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/951 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/951' -> `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)Nc1cc(S(=O)(=O)NC2CC2)ccc1O) `ZINC001597371034.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001597371034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597371034/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001597371034 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(S(=O)(=O)NC2CC2)ccc1O NO_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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 14, 11, 11, 8, 5, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] 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, 6, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 8, 4, 8, 8, 3, 3, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 10, 10, 10, 19, 34, 34, 6, 6, 6, 6, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 3, 3, 6, 19, 34, 34, 34, 34, 34, 6, 6, 12] 100 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: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597371034 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001597371034 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597371034/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597371034/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597371034 Building ZINC001597371034 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597371034' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597371034 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001597371034 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597371034/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597371034 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 950) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(S(=O)(=O)NC2CC2)ccc1O) `ZINC001597371034.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001597371034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597371034/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001597371034 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(S(=O)(=O)NC2CC2)ccc1O NO_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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 14, 11, 11, 8, 5, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] 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, 6, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 5, 7, 7, 3, 3, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 10, 10, 10, 19, 34, 34, 7, 7, 7, 7, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 3, 7, 19, 34, 34, 34, 34, 34, 7, 7, 14] 100 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: 150 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597371034 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597371034/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597371034 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 951) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(S(=O)(=O)NC2CC2)ccc1O) `ZINC001597371034.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001597371034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597371034/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001597371034 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(S(=O)(=O)NC2CC2)ccc1O NO_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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 14, 11, 11, 8, 5, 5, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] 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, 6, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 8, 4, 8, 8, 3, 3, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 10, 10, 10, 19, 34, 34, 6, 6, 6, 6, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 3, 3, 6, 19, 34, 34, 34, 34, 34, 6, 6, 12] 100 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: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597371034 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001597371034 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597371034/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597371034/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597371034 Building ZINC001597485431 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597485431' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597485431 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001597485431 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597485431/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597485431 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 952) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/952 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/952' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1sc(CNC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)nc1c1ccc(Cl)cc1) `ZINC001597485431.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001597485431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597485431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001597485431 none Cc1sc(CNC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)nc1c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'S.3', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', '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: [5, 1, 14, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 8, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 30, 30, 30, 31, 31, 30, 30, 31, 31, 30, 30, 30, 10, 10, 3, 1, 3, 3, 1, 1, 1, 1, 31, 31, 31, 31] 50 rigid atoms, others: [35, 38, 6, 39, 8, 9, 10, 11, 12, 13, 17, 18, 19, 41, 40] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 42, 43, 44, 45]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597485431 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597485431/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597485431 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 953) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/953 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/953' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1sc(CNC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)nc1c1ccc(Cl)cc1) `ZINC001597485431.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001597485431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597485431/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001597485431 none Cc1sc(CNC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)nc1c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'S.3', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', '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: [5, 1, 14, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 8, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 30, 30, 30, 31, 31, 31, 31, 31, 31, 30, 30, 30, 10, 10, 3, 1, 3, 3, 1, 1, 1, 1, 31, 31, 31, 31] 50 rigid atoms, others: [35, 38, 6, 39, 8, 9, 10, 11, 12, 13, 17, 18, 19, 41, 40] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 42, 43, 44, 45]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597485431 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001597485431 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597485431/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597485431/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597485431 Building ZINC001597485431 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597485431' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597485431 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001597485431 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597485431/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597485431 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 952) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1sc(CNC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)nc1c1ccc(Cl)cc1) `ZINC001597485431.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001597485431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597485431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001597485431 none Cc1sc(CNC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)nc1c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'S.3', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', '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: [5, 1, 14, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 8, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 30, 30, 30, 31, 31, 30, 30, 31, 31, 30, 30, 30, 10, 10, 3, 1, 3, 3, 1, 1, 1, 1, 31, 31, 31, 31] 50 rigid atoms, others: [35, 38, 6, 39, 8, 9, 10, 11, 12, 13, 17, 18, 19, 41, 40] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 42, 43, 44, 45]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597485431 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597485431/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597485431 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 953) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1sc(CNC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)nc1c1ccc(Cl)cc1) `ZINC001597485431.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001597485431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597485431/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001597485431 none Cc1sc(CNC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)nc1c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'S.3', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', '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: [5, 1, 14, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 8, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 30, 30, 30, 31, 31, 31, 31, 31, 31, 30, 30, 30, 10, 10, 3, 1, 3, 3, 1, 1, 1, 1, 31, 31, 31, 31] 50 rigid atoms, others: [35, 38, 6, 39, 8, 9, 10, 11, 12, 13, 17, 18, 19, 41, 40] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 42, 43, 44, 45]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597485431 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001597485431 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597485431/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597485431/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001597485431 Building ZINC001598052506 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001598052506' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001598052506 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001598052506 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001598052506/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001598052506 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 954) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/954 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/954' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1CCN(S(=O)(=O)c2ccccc2)CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001598052506.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001598052506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001598052506/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001598052506 none O=C(NCC1CCN(S(=O)(=O)c2ccccc2)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', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7] 0 hydrogens need 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, 16, 27, 27, 27, 27, 32, 32, 32, 33, 33, 32, 33, 33, 27, 27, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 13, 13, 27, 27, 27, 27, 27, 33, 33, 33, 33, 33, 27, 27, 27, 27, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001598052506 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001598052506/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001598052506 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 955) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/955 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/955' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1CCN(S(=O)(=O)c2ccccc2)CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001598052506.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001598052506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001598052506/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001598052506 none O=C(NCC1CCN(S(=O)(=O)c2ccccc2)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', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7] 0 hydrogens need 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, 27, 27, 27, 27, 32, 32, 32, 33, 33, 32, 33, 33, 27, 27, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 14, 14, 27, 27, 27, 27, 27, 33, 33, 32, 33, 33, 27, 27, 27, 27, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001598052506 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001598052506 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001598052506/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001598052506/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001598052506 Building ZINC001598052506 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001598052506' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001598052506 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001598052506 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001598052506/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001598052506 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 954) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/954: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1CCN(S(=O)(=O)c2ccccc2)CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001598052506.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001598052506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001598052506/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001598052506 none O=C(NCC1CCN(S(=O)(=O)c2ccccc2)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', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7] 0 hydrogens need 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, 16, 27, 27, 27, 27, 32, 32, 32, 33, 33, 32, 33, 33, 27, 27, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 13, 13, 27, 27, 27, 27, 27, 33, 33, 33, 33, 33, 27, 27, 27, 27, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001598052506 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001598052506/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001598052506 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 955) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/955: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1CCN(S(=O)(=O)c2ccccc2)CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001598052506.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001598052506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001598052506/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001598052506 none O=C(NCC1CCN(S(=O)(=O)c2ccccc2)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', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 6, 6, 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, 7, 7, 7] 0 hydrogens need 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, 27, 27, 27, 27, 32, 32, 32, 33, 33, 32, 33, 33, 27, 27, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 14, 14, 27, 27, 27, 27, 27, 33, 33, 32, 33, 33, 27, 27, 27, 27, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001598052506 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001598052506 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001598052506/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001598052506/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001598052506 Building ZINC001629334963 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001629334963 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 956) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/956 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/956' -> `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@H]1CC[N@](CC(=O)NC(C)(C)C)CC1) `ZINC001629334963.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001629334963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001629334963 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@](CC(=O)NC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 12, 28, 28, 28, 28, 28, 46, 48, 48, 48, 48, 48, 48, 28, 28, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 8, 8, 28, 28, 28, 28, 46, 46, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 28, 28, 28, 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, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 957) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/957 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/957' -> `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@H]1CC[N@](CC(=O)NC(C)(C)C)CC1) `ZINC001629334963.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001629334963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001629334963 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@](CC(=O)NC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 12, 27, 27, 27, 27, 27, 46, 47, 47, 47, 47, 47, 47, 27, 27, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 8, 8, 27, 27, 27, 27, 46, 46, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 27, 27, 27, 27] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 958) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/958 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/958' -> `2.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@H]1CC[N@@](CC(=O)NC(C)(C)C)CC1) `ZINC001629334963.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001629334963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001629334963 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@@](CC(=O)NC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 2, 12, 28, 28, 28, 28, 28, 45, 47, 47, 47, 47, 47, 47, 28, 28, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 2, 8, 8, 28, 28, 28, 28, 45, 45, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 28, 28, 28, 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, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 959) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/959 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/959' -> `3.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@H]1CC[N@@](CC(=O)NC(C)(C)C)CC1) `ZINC001629334963.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001629334963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001629334963 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@@](CC(=O)NC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 12, 28, 28, 28, 28, 28, 46, 47, 47, 47, 47, 47, 47, 28, 28, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 8, 8, 28, 28, 28, 28, 46, 46, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 28, 28, 28, 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, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001629334963 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963 Building ZINC001629334963 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001629334963 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 956) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@](CC(=O)NC(C)(C)C)CC1) `ZINC001629334963.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001629334963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001629334963 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@](CC(=O)NC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 12, 28, 28, 28, 28, 28, 46, 48, 48, 48, 48, 48, 48, 28, 28, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 8, 8, 28, 28, 28, 28, 46, 46, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 28, 28, 28, 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, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 957) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@](CC(=O)NC(C)(C)C)CC1) `ZINC001629334963.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001629334963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001629334963 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@](CC(=O)NC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 12, 27, 27, 27, 27, 27, 46, 47, 47, 47, 47, 47, 47, 27, 27, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 8, 8, 27, 27, 27, 27, 46, 46, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 27, 27, 27, 27] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 958) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/958: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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@H]1CC[N@@](CC(=O)NC(C)(C)C)CC1) `ZINC001629334963.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001629334963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001629334963 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@@](CC(=O)NC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 2, 12, 28, 28, 28, 28, 28, 45, 47, 47, 47, 47, 47, 47, 28, 28, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 2, 8, 8, 28, 28, 28, 28, 45, 45, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 28, 28, 28, 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, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 959) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/959: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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@H]1CC[N@@](CC(=O)NC(C)(C)C)CC1) `ZINC001629334963.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001629334963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001629334963 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@@](CC(=O)NC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 12, 28, 28, 28, 28, 28, 46, 47, 47, 47, 47, 47, 47, 28, 28, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 8, 8, 28, 28, 28, 28, 46, 46, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 28, 28, 28, 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, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001629334963 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963 Building ZINC001629334963 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001629334963 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 956) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@](CC(=O)NC(C)(C)C)CC1) `ZINC001629334963.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001629334963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001629334963 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@](CC(=O)NC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 12, 28, 28, 28, 28, 28, 46, 48, 48, 48, 48, 48, 48, 28, 28, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 8, 8, 28, 28, 28, 28, 46, 46, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 28, 28, 28, 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, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 957) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@](CC(=O)NC(C)(C)C)CC1) `ZINC001629334963.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001629334963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001629334963 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@](CC(=O)NC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 12, 27, 27, 27, 27, 27, 46, 47, 47, 47, 47, 47, 47, 27, 27, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 8, 8, 27, 27, 27, 27, 46, 46, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 27, 27, 27, 27] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 958) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/958: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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@H]1CC[N@@](CC(=O)NC(C)(C)C)CC1) `ZINC001629334963.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001629334963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001629334963 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@@](CC(=O)NC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 2, 12, 28, 28, 28, 28, 28, 45, 47, 47, 47, 47, 47, 47, 28, 28, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 2, 8, 8, 28, 28, 28, 28, 45, 45, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 28, 28, 28, 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, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 959) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/959: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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@H]1CC[N@@](CC(=O)NC(C)(C)C)CC1) `ZINC001629334963.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001629334963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001629334963 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@@](CC(=O)NC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 12, 28, 28, 28, 28, 28, 46, 47, 47, 47, 47, 47, 47, 28, 28, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 8, 8, 28, 28, 28, 28, 46, 46, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 28, 28, 28, 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, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001629334963 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963 Building ZINC001629334963 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001629334963 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 956) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@](CC(=O)NC(C)(C)C)CC1) `ZINC001629334963.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001629334963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001629334963 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@](CC(=O)NC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 12, 28, 28, 28, 28, 28, 46, 48, 48, 48, 48, 48, 48, 28, 28, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 8, 8, 28, 28, 28, 28, 46, 46, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 28, 28, 28, 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, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 957) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@](CC(=O)NC(C)(C)C)CC1) `ZINC001629334963.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001629334963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001629334963 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@](CC(=O)NC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 12, 27, 27, 27, 27, 27, 46, 47, 47, 47, 47, 47, 47, 27, 27, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 8, 8, 27, 27, 27, 27, 46, 46, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 27, 27, 27, 27] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 958) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/958: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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@H]1CC[N@@](CC(=O)NC(C)(C)C)CC1) `ZINC001629334963.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001629334963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001629334963 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@@](CC(=O)NC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 2, 12, 28, 28, 28, 28, 28, 45, 47, 47, 47, 47, 47, 47, 28, 28, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 2, 8, 8, 28, 28, 28, 28, 45, 45, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 28, 28, 28, 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, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 959) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/959: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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@H]1CC[N@@](CC(=O)NC(C)(C)C)CC1) `ZINC001629334963.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001629334963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001629334963 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[N@@](CC(=O)NC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 12, 28, 28, 28, 28, 28, 46, 47, 47, 47, 47, 47, 47, 28, 28, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 8, 8, 28, 28, 28, 28, 46, 46, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 28, 28, 28, 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, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001629334963 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001629334963 Building ZINC001630049760 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630049760' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630049760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001630049760 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630049760/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630049760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 960) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/960 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/960' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(n2c(NC(=O)[C@@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)nc3cc(C)ccc32)cc1) `ZINC001630049760.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001630049760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630049760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001630049760 none Cc1ccc(n2c(NC(=O)[C@@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)nc3cc(C)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'N.2', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 8, 1, 1, 1, 5, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 8, 8, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 19, 19, 19, 6, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 13, 13, 13, 13, 13, 13, 13, 4, 6, 19, 19, 6, 6, 6, 6, 8, 8, 8, 8, 8, 8, 13, 13] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 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/418326/xbt-8058088.46/working/building/ZINC001630049760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630049760/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630049760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 961) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/961 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/961' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(n2c(NC(=O)[C@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)nc3cc(C)ccc32)cc1) `ZINC001630049760.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001630049760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630049760/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001630049760 none Cc1ccc(n2c(NC(=O)[C@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)nc3cc(C)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'N.2', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 8, 1, 1, 1, 5, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 13, 13, 8, 8, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 19, 19, 19, 6, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 13, 13, 13, 13, 13, 13, 13, 4, 6, 19, 19, 6, 6, 6, 6, 8, 8, 8, 8, 8, 8, 13, 13] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 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/418326/xbt-8058088.46/working/building/ZINC001630049760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001630049760 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630049760/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630049760/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630049760 Building ZINC001630049760 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630049760' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630049760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001630049760 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630049760/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630049760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 960) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1ccc(n2c(NC(=O)[C@@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)nc3cc(C)ccc32)cc1) `ZINC001630049760.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001630049760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630049760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001630049760 none Cc1ccc(n2c(NC(=O)[C@@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)nc3cc(C)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'N.2', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 8, 1, 1, 1, 5, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 8, 8, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 19, 19, 19, 6, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 13, 13, 13, 13, 13, 13, 13, 4, 6, 19, 19, 6, 6, 6, 6, 8, 8, 8, 8, 8, 8, 13, 13] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 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/418326/xbt-8058088.46/working/building/ZINC001630049760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630049760/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630049760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 961) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1ccc(n2c(NC(=O)[C@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)nc3cc(C)ccc32)cc1) `ZINC001630049760.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001630049760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630049760/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001630049760 none Cc1ccc(n2c(NC(=O)[C@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)nc3cc(C)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'N.2', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 8, 1, 1, 1, 5, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 13, 13, 8, 8, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 19, 19, 19, 6, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 13, 13, 13, 13, 13, 13, 13, 4, 6, 19, 19, 6, 6, 6, 6, 8, 8, 8, 8, 8, 8, 13, 13] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 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/418326/xbt-8058088.46/working/building/ZINC001630049760 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001630049760 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630049760/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630049760/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630049760 Building ZINC001630146139 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630146139' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630146139 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001630146139 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630146139/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630146139 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 962) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/962 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/962' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H](O)COc1ccc2c(c1)CCC(=O)N2)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001630146139.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001630146139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630146139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001630146139 none O=C(NC[C@@H](O)COc1ccc2c(c1)CCC(=O)N2)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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, 5, 5, 7, 12, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 10, 16, 16, 16, 16, 27, 42, 43, 43, 43, 42, 43, 43, 43, 43, 43, 1, 1, 1, 5, 5, 5, 5, 5, 2, 10, 10, 48, 16, 16, 43, 43, 43, 43, 43, 43, 43, 43, 5, 5] 150 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 180 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630146139 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630146139/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630146139 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 963) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/963 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/963' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H](O)COc1ccc2c(c1)CCC(=O)N2)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001630146139.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001630146139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630146139/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001630146139 none O=C(NC[C@@H](O)COc1ccc2c(c1)CCC(=O)N2)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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, 5, 5, 7, 12, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 9, 13, 13, 13, 13, 27, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 5, 5, 5, 5, 5, 3, 9, 9, 39, 13, 13, 44, 44, 44, 44, 44, 44, 44, 44, 5, 5] 150 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630146139 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001630146139 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630146139/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630146139/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630146139 Building ZINC001630146139 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630146139' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630146139 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001630146139 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630146139/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630146139 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 962) grep: /scratch/xiaobo/418326/xbt-8058088.46/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(NC[C@@H](O)COc1ccc2c(c1)CCC(=O)N2)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001630146139.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001630146139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630146139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001630146139 none O=C(NC[C@@H](O)COc1ccc2c(c1)CCC(=O)N2)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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, 5, 5, 7, 12, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 10, 16, 16, 16, 16, 27, 42, 43, 43, 43, 42, 43, 43, 43, 43, 43, 1, 1, 1, 5, 5, 5, 5, 5, 2, 10, 10, 48, 16, 16, 43, 43, 43, 43, 43, 43, 43, 43, 5, 5] 150 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 180 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630146139 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630146139/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630146139 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 963) grep: /scratch/xiaobo/418326/xbt-8058088.46/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(NC[C@@H](O)COc1ccc2c(c1)CCC(=O)N2)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001630146139.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001630146139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630146139/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001630146139 none O=C(NC[C@@H](O)COc1ccc2c(c1)CCC(=O)N2)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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, 5, 5, 7, 12, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 9, 13, 13, 13, 13, 27, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 5, 5, 5, 5, 5, 3, 9, 9, 39, 13, 13, 44, 44, 44, 44, 44, 44, 44, 44, 5, 5] 150 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630146139 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001630146139 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630146139/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630146139/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630146139 Building ZINC001630146140 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630146140' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630146140 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001630146140 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630146140/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630146140 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 964) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/964 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/964' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H](O)COc1ccc2c(c1)CCC(=O)N2)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001630146140.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001630146140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630146140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001630146140 none O=C(NC[C@H](O)COc1ccc2c(c1)CCC(=O)N2)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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, 5, 5, 7, 12, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 9, 13, 13, 13, 13, 27, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 5, 5, 5, 5, 5, 3, 9, 9, 39, 13, 13, 44, 44, 44, 44, 44, 44, 44, 44, 5, 5] 150 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630146140 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630146140/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630146140 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 965) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/965 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/965' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H](O)COc1ccc2c(c1)CCC(=O)N2)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001630146140.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001630146140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630146140/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001630146140 none O=C(NC[C@H](O)COc1ccc2c(c1)CCC(=O)N2)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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, 5, 5, 7, 12, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 10, 16, 16, 16, 16, 27, 42, 43, 43, 43, 42, 43, 43, 43, 43, 43, 1, 1, 1, 5, 5, 5, 5, 5, 2, 10, 10, 48, 16, 16, 43, 43, 43, 43, 43, 43, 43, 43, 5, 5] 150 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 180 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630146140 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001630146140 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630146140/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630146140/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630146140 Building ZINC001630146140 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630146140' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630146140 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001630146140 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630146140/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630146140 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 964) grep: /scratch/xiaobo/418326/xbt-8058088.46/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(NC[C@H](O)COc1ccc2c(c1)CCC(=O)N2)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001630146140.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001630146140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630146140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001630146140 none O=C(NC[C@H](O)COc1ccc2c(c1)CCC(=O)N2)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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, 5, 5, 7, 12, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 9, 13, 13, 13, 13, 27, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 5, 5, 5, 5, 5, 3, 9, 9, 39, 13, 13, 44, 44, 44, 44, 44, 44, 44, 44, 5, 5] 150 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630146140 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630146140/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630146140 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 965) grep: /scratch/xiaobo/418326/xbt-8058088.46/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(NC[C@H](O)COc1ccc2c(c1)CCC(=O)N2)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001630146140.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001630146140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630146140/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001630146140 none O=C(NC[C@H](O)COc1ccc2c(c1)CCC(=O)N2)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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, 5, 5, 7, 12, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 10, 16, 16, 16, 16, 27, 42, 43, 43, 43, 42, 43, 43, 43, 43, 43, 1, 1, 1, 5, 5, 5, 5, 5, 2, 10, 10, 48, 16, 16, 43, 43, 43, 43, 43, 43, 43, 43, 5, 5] 150 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 180 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630146140 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001630146140 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630146140/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630146140/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630146140 Building ZINC001630425082 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630425082' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630425082 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001630425082 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630425082/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630425082 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 966) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/966 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/966' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc2nc(c3cc(F)ccc3F)[nH]c2c1) `ZINC001630425082.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001630425082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630425082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001630425082 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc2nc(c3cc(F)ccc3F)[nH]c2c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.pl3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 1, 15, 8, 6, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 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, 12, 4, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 10, 10, 15, 15, 15, 15, 15, 15, 15, 10, 10, 10, 10, 4, 4, 4, 4, 12, 12, 4, 2, 10, 10, 15, 15, 15, 10] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630425082 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630425082/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630425082 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 967) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/967 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/967' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc2nc(c3cc(F)ccc3F)[nH]c2c1) `ZINC001630425082.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001630425082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630425082/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001630425082 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc2nc(c3cc(F)ccc3F)[nH]c2c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.pl3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 1, 15, 8, 6, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 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, 11, 4, 1, 1, 1, 1, 2, 2, 2, 11, 11, 11, 11, 11, 11, 16, 16, 16, 16, 16, 16, 16, 11, 11, 11, 11, 4, 4, 4, 4, 11, 11, 4, 2, 11, 11, 16, 16, 16, 11] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630425082 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001630425082 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630425082/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630425082/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630425082 Building ZINC001630425082 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630425082' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630425082 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001630425082 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630425082/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630425082 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 966) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc2nc(c3cc(F)ccc3F)[nH]c2c1) `ZINC001630425082.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001630425082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630425082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001630425082 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc2nc(c3cc(F)ccc3F)[nH]c2c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.pl3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 1, 15, 8, 6, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 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, 12, 4, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 10, 10, 15, 15, 15, 15, 15, 15, 15, 10, 10, 10, 10, 4, 4, 4, 4, 12, 12, 4, 2, 10, 10, 15, 15, 15, 10] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630425082 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630425082/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630425082 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 967) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc2nc(c3cc(F)ccc3F)[nH]c2c1) `ZINC001630425082.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001630425082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630425082/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001630425082 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc2nc(c3cc(F)ccc3F)[nH]c2c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.pl3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 1, 15, 8, 6, 1, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 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, 11, 4, 1, 1, 1, 1, 2, 2, 2, 11, 11, 11, 11, 11, 11, 16, 16, 16, 16, 16, 16, 16, 11, 11, 11, 11, 4, 4, 4, 4, 11, 11, 4, 2, 11, 11, 16, 16, 16, 11] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630425082 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001630425082 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630425082/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630425082/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630425082 Building ZINC001630635110 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630635110' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630635110 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001630635110 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630635110/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630635110 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 968) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/968 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/968' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(COc2cccc(NC(=O)[C@@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)c2C)c1) `ZINC001630635110.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001630635110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630635110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001630635110 none COc1cccc(COc2cccc(NC(=O)[C@@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 47, 24, 10, 5, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 5, 5, 47, 47, 47, 47, 47, 47, 47, 24, 24, 5, 5, 5, 2, 1, 3, 3, 1, 1, 1, 1, 5, 5, 5, 47] 50 rigid atoms, others: [49, 47, 44, 50, 15, 48, 17, 18, 19, 20, 21, 22, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 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/418326/xbt-8058088.46/working/building/ZINC001630635110 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630635110/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630635110 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 969) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/969 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/969' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(COc2cccc(NC(=O)[C@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)c2C)c1) `ZINC001630635110.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001630635110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630635110/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001630635110 none COc1cccc(COc2cccc(NC(=O)[C@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 46, 46, 46, 24, 10, 5, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 5, 5, 46, 46, 46, 46, 46, 46, 46, 24, 24, 5, 5, 5, 2, 1, 3, 3, 1, 1, 1, 1, 5, 5, 5, 46] 50 rigid atoms, others: [49, 47, 44, 50, 15, 48, 17, 18, 19, 20, 21, 22, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 51, 52, 53, 54]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630635110 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001630635110 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630635110/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630635110/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630635110 Building ZINC001630635110 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630635110' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630635110 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001630635110 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630635110/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630635110 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 968) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cccc(COc2cccc(NC(=O)[C@@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)c2C)c1) `ZINC001630635110.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001630635110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630635110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001630635110 none COc1cccc(COc2cccc(NC(=O)[C@@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 47, 24, 10, 5, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 5, 5, 47, 47, 47, 47, 47, 47, 47, 24, 24, 5, 5, 5, 2, 1, 3, 3, 1, 1, 1, 1, 5, 5, 5, 47] 50 rigid atoms, others: [49, 47, 44, 50, 15, 48, 17, 18, 19, 20, 21, 22, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 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/418326/xbt-8058088.46/working/building/ZINC001630635110 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630635110/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630635110 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 969) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1cccc(COc2cccc(NC(=O)[C@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)c2C)c1) `ZINC001630635110.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001630635110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630635110/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001630635110 none COc1cccc(COc2cccc(NC(=O)[C@]([O-])([SiH3])c3cc(S(N)(=O)=O)cn3C)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 46, 46, 46, 24, 10, 5, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 5, 5, 46, 46, 46, 46, 46, 46, 46, 24, 24, 5, 5, 5, 2, 1, 3, 3, 1, 1, 1, 1, 5, 5, 5, 46] 50 rigid atoms, others: [49, 47, 44, 50, 15, 48, 17, 18, 19, 20, 21, 22, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 51, 52, 53, 54]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630635110 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001630635110 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630635110/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630635110/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001630635110 Building ZINC001631383009 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631383009' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631383009 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631383009 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631383009/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631383009 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 970) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/970 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/970' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2c(c1)CN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H](c1ccccc1)C2) `ZINC001631383009.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631383009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631383009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001631383009 none COc1ccc2c(c1)CN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H](c1ccccc1)C2 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.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', '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, 12, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 8, 8, 8, 8, 8, 8, 8, 8, 6, 2, 6, 1, 1, 1, 2, 2, 2, 8, 8, 8, 2, 2, 2, 8, 8, 8, 12, 12, 9, 12, 12, 8, 13, 13, 13, 8, 8, 8, 8, 8, 2, 8, 8, 2, 2, 2, 2, 12, 12, 12, 12, 12, 8, 8] 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: 76 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631383009 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631383009/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631383009 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 971) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/971 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/971' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2c(c1)CN(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H](c1ccccc1)C2) `ZINC001631383009.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631383009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631383009/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001631383009 none COc1ccc2c(c1)CN(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H](c1ccccc1)C2 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.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', '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, 12, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 12, 12, 12, 8, 1, 8, 1, 1, 1, 3, 3, 3, 8, 8, 8, 3, 3, 3, 12, 12, 12, 16, 16, 12, 16, 16, 12, 17, 17, 17, 12, 12, 12, 12, 12, 3, 8, 8, 3, 3, 3, 3, 16, 16, 12, 16, 16, 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]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631383009 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001631383009 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631383009/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631383009/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631383009 Building ZINC001631383009 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631383009' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631383009 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631383009 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631383009/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631383009 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 970) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2c(c1)CN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H](c1ccccc1)C2) `ZINC001631383009.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631383009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631383009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001631383009 none COc1ccc2c(c1)CN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H](c1ccccc1)C2 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.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', '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, 12, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 8, 8, 8, 8, 8, 8, 8, 8, 6, 2, 6, 1, 1, 1, 2, 2, 2, 8, 8, 8, 2, 2, 2, 8, 8, 8, 12, 12, 9, 12, 12, 8, 13, 13, 13, 8, 8, 8, 8, 8, 2, 8, 8, 2, 2, 2, 2, 12, 12, 12, 12, 12, 8, 8] 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: 76 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631383009 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631383009/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631383009 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 971) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2c(c1)CN(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H](c1ccccc1)C2) `ZINC001631383009.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631383009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631383009/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001631383009 none COc1ccc2c(c1)CN(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H](c1ccccc1)C2 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.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', '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, 12, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 12, 12, 12, 8, 1, 8, 1, 1, 1, 3, 3, 3, 8, 8, 8, 3, 3, 3, 12, 12, 12, 16, 16, 12, 16, 16, 12, 17, 17, 17, 12, 12, 12, 12, 12, 3, 8, 8, 3, 3, 3, 3, 16, 16, 12, 16, 16, 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]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631383009 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001631383009 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631383009/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631383009/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631383009 Building ZINC001631383010 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631383010' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631383010 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631383010 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631383010/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631383010 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 972) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/972 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/972' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2c(c1)CN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@@H](c1ccccc1)C2) `ZINC001631383010.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631383010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631383010/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001631383010 none COc1ccc2c(c1)CN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@@H](c1ccccc1)C2 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.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', '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, 12, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 8, 8, 8, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 4, 4, 4, 15, 15, 15, 4, 4, 4, 8, 8, 8, 10, 10, 8, 10, 10, 8, 11, 11, 11, 8, 8, 8, 8, 8, 4, 15, 15, 4, 4, 4, 4, 10, 10, 8, 10, 10, 8, 8] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 81 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631383010 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631383010/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631383010 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 973) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/973 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/973' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2c(c1)CN(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@@H](c1ccccc1)C2) `ZINC001631383010.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631383010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631383010/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001631383010 none COc1ccc2c(c1)CN(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@@H](c1ccccc1)C2 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.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', '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, 12, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 4, 4, 4, 15, 15, 15, 4, 4, 4, 6, 6, 6, 8, 8, 6, 8, 8, 6, 8, 8, 8, 6, 6, 6, 6, 6, 4, 15, 15, 4, 4, 4, 4, 8, 8, 6, 8, 8, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 76 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631383010 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001631383010 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631383010/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631383010/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631383010 Building ZINC001631383010 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631383010' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631383010 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631383010 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631383010/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631383010 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 972) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2c(c1)CN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@@H](c1ccccc1)C2) `ZINC001631383010.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631383010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631383010/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001631383010 none COc1ccc2c(c1)CN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@@H](c1ccccc1)C2 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.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', '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, 12, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 8, 8, 8, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 4, 4, 4, 15, 15, 15, 4, 4, 4, 8, 8, 8, 10, 10, 8, 10, 10, 8, 11, 11, 11, 8, 8, 8, 8, 8, 4, 15, 15, 4, 4, 4, 4, 10, 10, 8, 10, 10, 8, 8] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 81 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631383010 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631383010/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631383010 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 973) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: COc1ccc2c(c1)CN(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@@H](c1ccccc1)C2) `ZINC001631383010.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631383010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631383010/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001631383010 none COc1ccc2c(c1)CN(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@@H](c1ccccc1)C2 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.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', '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, 12, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 4, 4, 4, 15, 15, 15, 4, 4, 4, 6, 6, 6, 8, 8, 6, 8, 8, 6, 8, 8, 8, 6, 6, 6, 6, 6, 4, 15, 15, 4, 4, 4, 4, 8, 8, 6, 8, 8, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 76 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631383010 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001631383010 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631383010/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631383010/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631383010 Building ZINC001631573513 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631573513' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631573513 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631573513 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631573513/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631573513 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 974) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/974 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/974' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(c2ncc(I)cn2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001631573513.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631573513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631573513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001631573513 none O=C(N1CCN(c2ncc(I)cn2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'N.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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 8, 1, 1, 18, 1, 8, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 2, 20, 33, 33, 33, 33, 47, 47, 33, 38, 47, 47, 33, 33, 1, 1, 1, 4, 4, 1, 1, 4, 4, 33, 33, 33, 33, 47, 47, 33, 33, 33, 33, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631573513 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631573513/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631573513 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 975) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/975 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/975' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(c2ncc(I)cn2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001631573513.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631573513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631573513/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001631573513 none O=C(N1CCN(c2ncc(I)cn2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'N.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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 8, 1, 1, 18, 1, 8, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 21, 33, 33, 33, 33, 47, 47, 33, 45, 47, 47, 33, 33, 1, 1, 1, 4, 4, 1, 1, 4, 4, 33, 33, 33, 33, 47, 47, 33, 33, 33, 33, 4, 4, 4, 4] 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, 37]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631573513 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001631573513 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631573513/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631573513/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631573513 Building ZINC001631573513 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631573513' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631573513 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631573513 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631573513/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631573513 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 974) grep: /scratch/xiaobo/418326/xbt-8058088.46/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(N1CCN(c2ncc(I)cn2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001631573513.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631573513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631573513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001631573513 none O=C(N1CCN(c2ncc(I)cn2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'N.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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 8, 1, 1, 18, 1, 8, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 2, 20, 33, 33, 33, 33, 47, 47, 33, 38, 47, 47, 33, 33, 1, 1, 1, 4, 4, 1, 1, 4, 4, 33, 33, 33, 33, 47, 47, 33, 33, 33, 33, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631573513 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631573513/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631573513 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 975) grep: /scratch/xiaobo/418326/xbt-8058088.46/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(N1CCN(c2ncc(I)cn2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001631573513.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631573513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631573513/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001631573513 none O=C(N1CCN(c2ncc(I)cn2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'N.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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 8, 1, 1, 18, 1, 8, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 21, 33, 33, 33, 33, 47, 47, 33, 45, 47, 47, 33, 33, 1, 1, 1, 4, 4, 1, 1, 4, 4, 33, 33, 33, 33, 47, 47, 33, 33, 33, 33, 4, 4, 4, 4] 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, 37]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631573513 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001631573513 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631573513/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631573513/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631573513 Building ZINC001631667975 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631667975' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631667975 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631667975 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631667975/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631667975 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 976) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/976 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/976' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)nn1c1ccc(Cl)cc1Cl) `ZINC001631667975.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631667975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631667975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001631667975 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)nn1c1ccc(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 11, 11, 11, 4, 4, 4, 7, 7, 7, 13, 13, 7, 13, 13, 13, 13, 7, 7, 7, 7, 3, 4, 11, 11, 4, 4, 4, 4, 13, 13, 13] 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: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631667975 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631667975/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631667975 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 977) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/977 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/977' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)nn1c1ccc(Cl)cc1Cl) `ZINC001631667975.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631667975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631667975/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001631667975 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)nn1c1ccc(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 11, 11, 11, 4, 4, 4, 7, 7, 7, 13, 13, 13, 13, 13, 13, 13, 7, 7, 7, 7, 3, 4, 11, 11, 4, 4, 4, 4, 13, 13, 13] 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: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631667975 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001631667975 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631667975/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631667975/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631667975 Building ZINC001631667975 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631667975' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631667975 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631667975 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631667975/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631667975 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 976) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)nn1c1ccc(Cl)cc1Cl) `ZINC001631667975.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631667975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631667975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001631667975 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)nn1c1ccc(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 11, 11, 11, 4, 4, 4, 7, 7, 7, 13, 13, 7, 13, 13, 13, 13, 7, 7, 7, 7, 3, 4, 11, 11, 4, 4, 4, 4, 13, 13, 13] 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: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631667975 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631667975/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631667975 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 977) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)nn1c1ccc(Cl)cc1Cl) `ZINC001631667975.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631667975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631667975/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001631667975 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)nn1c1ccc(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 11, 11, 11, 4, 4, 4, 7, 7, 7, 13, 13, 13, 13, 13, 13, 13, 7, 7, 7, 7, 3, 4, 11, 11, 4, 4, 4, 4, 13, 13, 13] 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: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631667975 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001631667975 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631667975/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631667975/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631667975 Building ZINC001631916456 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631916456' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631916456 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631916456 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631916456/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631916456 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 978) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/978 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/978' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCCCc1cc(c2ccccc2)no1)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001631916456.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631916456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631916456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001631916456 none CN(CCCCCc1cc(c2ccccc2)no1)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', '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', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 6, 7, 7, 7, 7, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 2, 2, 2, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 25, 25, 25, 25, 25, 25, 1, 4, 4, 1, 1, 1, 1] 50 rigid atoms, others: [1, 54, 51, 57, 55, 56, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 53]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631916456 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631916456/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631916456 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 979) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/979 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/979' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCCCc1cc(c2ccccc2)no1)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001631916456.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631916456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631916456/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001631916456 none CN(CCCCCc1cc(c2ccccc2)no1)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', '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', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 6, 7, 7, 7, 7, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 2, 2, 2, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 25, 25, 25, 25, 25, 25, 1, 4, 4, 1, 1, 1, 1] 50 rigid atoms, others: [1, 54, 51, 57, 55, 56, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 53]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631916456 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001631916456 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631916456/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631916456/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631916456 Building ZINC001631916456 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631916456' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631916456 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001631916456 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631916456/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631916456 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 978) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CN(CCCCCc1cc(c2ccccc2)no1)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001631916456.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001631916456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631916456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001631916456 none CN(CCCCCc1cc(c2ccccc2)no1)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', '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', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 6, 7, 7, 7, 7, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 2, 2, 2, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 25, 25, 25, 25, 25, 25, 1, 4, 4, 1, 1, 1, 1] 50 rigid atoms, others: [1, 54, 51, 57, 55, 56, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 53]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631916456 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631916456/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631916456 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 979) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CN(CCCCCc1cc(c2ccccc2)no1)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001631916456.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001631916456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631916456/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001631916456 none CN(CCCCCc1cc(c2ccccc2)no1)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', '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', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 6, 7, 7, 7, 7, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 2, 2, 2, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 25, 25, 25, 25, 25, 25, 1, 4, 4, 1, 1, 1, 1] 50 rigid atoms, others: [1, 54, 51, 57, 55, 56, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 53]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631916456 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001631916456 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631916456/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631916456/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001631916456 Building ZINC001632437985 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632437985' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632437985 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632437985 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632437985/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632437985 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 980) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/980 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/980' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1cc(F)cc(Br)c1) `ZINC001632437985.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632437985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632437985/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001632437985 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1cc(F)cc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 15, 1, 1, 17, 1, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 3, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15, 15, 15, 3, 3, 3, 3, 8, 8, 3, 5, 5, 5, 5, 5, 5, 15, 15, 15] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 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: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632437985 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632437985/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632437985 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 981) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/981 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/981' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1cc(F)cc(Br)c1) `ZINC001632437985.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632437985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632437985/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001632437985 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1cc(F)cc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 15, 1, 1, 17, 1, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 6, 2, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 2, 2, 2, 2, 6, 6, 2, 8, 8, 8, 8, 8, 8, 22, 22, 22] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 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: 59 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632437985 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001632437985 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632437985/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632437985/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632437985 Building ZINC001632437985 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632437985' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632437985 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632437985 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632437985/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632437985 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 980) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1cc(F)cc(Br)c1) `ZINC001632437985.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632437985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632437985/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001632437985 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1cc(F)cc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 15, 1, 1, 17, 1, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 3, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15, 15, 15, 3, 3, 3, 3, 8, 8, 3, 5, 5, 5, 5, 5, 5, 15, 15, 15] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 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: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632437985 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632437985/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632437985 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 981) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1cc(F)cc(Br)c1) `ZINC001632437985.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632437985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632437985/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001632437985 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1cc(F)cc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 15, 1, 1, 17, 1, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 6, 2, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 2, 2, 2, 2, 6, 6, 2, 8, 8, 8, 8, 8, 8, 22, 22, 22] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 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: 59 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632437985 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001632437985 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632437985/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632437985/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632437985 Building ZINC001632437986 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632437986' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632437986 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632437986 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632437986/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632437986 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 982) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/982 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/982' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1cc(F)cc(Br)c1) `ZINC001632437986.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632437986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632437986/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001632437986 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1cc(F)cc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 15, 1, 1, 17, 1, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 6, 2, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 8, 8, 22, 22, 22, 18, 22, 22, 22, 2, 2, 2, 2, 6, 6, 2, 8, 8, 8, 8, 8, 8, 22, 22, 22] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 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: 76 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632437986 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632437986/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632437986 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 983) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/983 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/983' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1cc(F)cc(Br)c1) `ZINC001632437986.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632437986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632437986/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001632437986 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1cc(F)cc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 15, 1, 1, 17, 1, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 6, 3, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 15, 15, 15, 13, 15, 15, 15, 3, 3, 3, 3, 6, 6, 3, 5, 5, 5, 5, 5, 5, 15, 15, 15] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 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: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632437986 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001632437986 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632437986/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632437986/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632437986 Building ZINC001632437986 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632437986' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632437986 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632437986 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632437986/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632437986 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 982) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1cc(F)cc(Br)c1) `ZINC001632437986.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632437986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632437986/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001632437986 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1cc(F)cc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 15, 1, 1, 17, 1, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 6, 2, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 8, 8, 22, 22, 22, 18, 22, 22, 22, 2, 2, 2, 2, 6, 6, 2, 8, 8, 8, 8, 8, 8, 22, 22, 22] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 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: 76 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632437986 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632437986/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632437986 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 983) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1cc(F)cc(Br)c1) `ZINC001632437986.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632437986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632437986/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001632437986 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1cc(F)cc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', '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', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 15, 1, 1, 17, 1, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 6, 3, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 15, 15, 15, 13, 15, 15, 15, 3, 3, 3, 3, 6, 6, 3, 5, 5, 5, 5, 5, 5, 15, 15, 15] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 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: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632437986 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001632437986 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632437986/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632437986/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632437986 Building ZINC001632760566 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632760566' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632760566 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632760566 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632760566/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632760566 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 984) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/984 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/984' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H](c1ccccc1C(F)(F)F)C(F)(F)F) `ZINC001632760566.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632760566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632760566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001632760566 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H](c1ccccc1C(F)(F)F)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', '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.3', 'F', 'F', 'F', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 18, 18, 18, 6, 1, 1, 1, 1, 4, 4, 4, 7, 7, 9, 9, 7, 9, 9, 9, 9, 9, 9, 7, 7, 7, 7, 6, 6, 6, 6, 18, 18, 6, 4, 9, 9, 7, 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]) total number of confs: 97 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632760566 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632760566/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632760566 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 985) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/985 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/985' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H](c1ccccc1C(F)(F)F)C(F)(F)F) `ZINC001632760566.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632760566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632760566/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001632760566 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H](c1ccccc1C(F)(F)F)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', '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.3', 'F', 'F', 'F', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 18, 18, 18, 5, 1, 1, 1, 1, 4, 4, 4, 7, 7, 10, 10, 7, 10, 10, 10, 10, 10, 10, 7, 7, 7, 7, 5, 5, 5, 5, 18, 18, 5, 4, 10, 10, 7, 10] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 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: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632760566 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001632760566 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632760566/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632760566/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632760566 Building ZINC001632760566 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632760566' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632760566 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632760566 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632760566/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632760566 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 984) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/984: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H](c1ccccc1C(F)(F)F)C(F)(F)F) `ZINC001632760566.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632760566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632760566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001632760566 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H](c1ccccc1C(F)(F)F)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', '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.3', 'F', 'F', 'F', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 18, 18, 18, 6, 1, 1, 1, 1, 4, 4, 4, 7, 7, 9, 9, 7, 9, 9, 9, 9, 9, 9, 7, 7, 7, 7, 6, 6, 6, 6, 18, 18, 6, 4, 9, 9, 7, 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]) total number of confs: 97 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632760566 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632760566/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632760566 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 985) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/985: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H](c1ccccc1C(F)(F)F)C(F)(F)F) `ZINC001632760566.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632760566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632760566/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001632760566 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H](c1ccccc1C(F)(F)F)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', '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.3', 'F', 'F', 'F', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 18, 18, 18, 5, 1, 1, 1, 1, 4, 4, 4, 7, 7, 10, 10, 7, 10, 10, 10, 10, 10, 10, 7, 7, 7, 7, 5, 5, 5, 5, 18, 18, 5, 4, 10, 10, 7, 10] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 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: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632760566 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001632760566 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632760566/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632760566/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632760566 Building ZINC001632760567 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632760567' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632760567 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632760567 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632760567/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632760567 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 986) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/986 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/986' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1ccccc1C(F)(F)F)C(F)(F)F) `ZINC001632760567.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632760567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632760567/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001632760567 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1ccccc1C(F)(F)F)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', '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.3', 'F', 'F', 'F', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 18, 18, 18, 5, 1, 1, 1, 1, 4, 4, 4, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 7, 7, 7, 5, 5, 5, 5, 18, 18, 5, 4, 9, 9, 9, 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]) total number of confs: 90 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632760567 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632760567/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632760567 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 987) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/987 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/987' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H](c1ccccc1C(F)(F)F)C(F)(F)F) `ZINC001632760567.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632760567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632760567/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001632760567 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H](c1ccccc1C(F)(F)F)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', '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.3', 'F', 'F', 'F', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 19, 19, 19, 6, 1, 1, 1, 1, 4, 4, 4, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 7, 7, 7, 6, 6, 6, 6, 19, 19, 6, 4, 9, 9, 9, 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]) total number of confs: 94 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632760567 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001632760567 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632760567/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632760567/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632760567 Building ZINC001632760567 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632760567' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632760567 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001632760567 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632760567/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632760567 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 986) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1ccccc1C(F)(F)F)C(F)(F)F) `ZINC001632760567.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001632760567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632760567/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001632760567 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1ccccc1C(F)(F)F)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', '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.3', 'F', 'F', 'F', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 18, 18, 18, 5, 1, 1, 1, 1, 4, 4, 4, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 7, 7, 7, 5, 5, 5, 5, 18, 18, 5, 4, 9, 9, 9, 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]) total number of confs: 90 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632760567 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632760567/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632760567 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 987) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H](c1ccccc1C(F)(F)F)C(F)(F)F) `ZINC001632760567.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001632760567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632760567/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001632760567 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H](c1ccccc1C(F)(F)F)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', '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.3', 'F', 'F', 'F', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 19, 19, 19, 6, 1, 1, 1, 1, 4, 4, 4, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 7, 7, 7, 6, 6, 6, 6, 19, 19, 6, 4, 9, 9, 9, 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]) total number of confs: 94 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632760567 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001632760567 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632760567/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632760567/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001632760567 Building ZINC001633010249 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001633010249 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 988) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/988 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/988' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCC[N@]1CC[N@](c2ncccn2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001633010249.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633010249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001633010249 none O=C(NCCCC[N@]1CC[N@](c2ncccn2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 2, 10, 15, 18, 28, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 3, 3, 3, 3, 3, 2, 10, 10, 18, 18, 18, 18, 26, 26, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 3, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 989) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/989 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/989' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCC[N@]1CC[N@@](c2ncccn2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001633010249.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633010249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001633010249 none O=C(NCCCC[N@]1CC[N@@](c2ncccn2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 2, 10, 15, 18, 29, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 3, 3, 3, 3, 3, 2, 10, 10, 18, 18, 18, 18, 27, 27, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 3, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 990) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/990 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/990' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCC[N@]1CC[N@](c2ncccn2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001633010249.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001633010249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001633010249 none O=C(NCCCC[N@]1CC[N@](c2ncccn2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 2, 10, 16, 19, 31, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 3, 3, 3, 3, 3, 2, 10, 10, 19, 19, 19, 19, 28, 28, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 3, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 991) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/991 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/991' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCC[N@]1CC[N@@](c2ncccn2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001633010249.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001633010249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001633010249 none O=C(NCCCC[N@]1CC[N@@](c2ncccn2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 2, 10, 16, 19, 31, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 3, 3, 3, 3, 3, 2, 10, 10, 19, 19, 19, 19, 28, 28, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 3, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001633010249 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249 Building ZINC001633010249 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001633010249 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 988) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: O=C(NCCCC[N@]1CC[N@](c2ncccn2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001633010249.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633010249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001633010249 none O=C(NCCCC[N@]1CC[N@](c2ncccn2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 2, 10, 15, 18, 28, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 3, 3, 3, 3, 3, 2, 10, 10, 18, 18, 18, 18, 26, 26, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 3, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 989) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: O=C(NCCCC[N@]1CC[N@@](c2ncccn2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001633010249.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633010249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001633010249 none O=C(NCCCC[N@]1CC[N@@](c2ncccn2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 2, 10, 15, 18, 29, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 3, 3, 3, 3, 3, 2, 10, 10, 18, 18, 18, 18, 27, 27, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 3, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 990) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: O=C(NCCCC[N@]1CC[N@](c2ncccn2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001633010249.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001633010249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001633010249 none O=C(NCCCC[N@]1CC[N@](c2ncccn2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 2, 10, 16, 19, 31, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 3, 3, 3, 3, 3, 2, 10, 10, 19, 19, 19, 19, 28, 28, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 3, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 991) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: O=C(NCCCC[N@]1CC[N@@](c2ncccn2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001633010249.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001633010249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001633010249 none O=C(NCCCC[N@]1CC[N@@](c2ncccn2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 2, 10, 16, 19, 31, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 3, 3, 3, 3, 3, 2, 10, 10, 19, 19, 19, 19, 28, 28, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 3, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001633010249 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249 Building ZINC001633010249 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001633010249 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 988) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: O=C(NCCCC[N@]1CC[N@](c2ncccn2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001633010249.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633010249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001633010249 none O=C(NCCCC[N@]1CC[N@](c2ncccn2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 2, 10, 15, 18, 28, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 3, 3, 3, 3, 3, 2, 10, 10, 18, 18, 18, 18, 26, 26, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 3, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 989) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: O=C(NCCCC[N@]1CC[N@@](c2ncccn2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001633010249.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633010249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001633010249 none O=C(NCCCC[N@]1CC[N@@](c2ncccn2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 2, 10, 15, 18, 29, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 3, 3, 3, 3, 3, 2, 10, 10, 18, 18, 18, 18, 27, 27, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 3, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 990) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: O=C(NCCCC[N@]1CC[N@](c2ncccn2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001633010249.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001633010249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001633010249 none O=C(NCCCC[N@]1CC[N@](c2ncccn2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 2, 10, 16, 19, 31, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 3, 3, 3, 3, 3, 2, 10, 10, 19, 19, 19, 19, 28, 28, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 3, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 991) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: O=C(NCCCC[N@]1CC[N@@](c2ncccn2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001633010249.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001633010249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001633010249 none O=C(NCCCC[N@]1CC[N@@](c2ncccn2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 2, 10, 16, 19, 31, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 3, 3, 3, 3, 3, 2, 10, 10, 19, 19, 19, 19, 28, 28, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 3, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001633010249 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249 Building ZINC001633010249 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001633010249 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 988) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: O=C(NCCCC[N@]1CC[N@](c2ncccn2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001633010249.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633010249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001633010249 none O=C(NCCCC[N@]1CC[N@](c2ncccn2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 2, 10, 15, 18, 28, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 3, 3, 3, 3, 3, 2, 10, 10, 18, 18, 18, 18, 26, 26, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 3, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 989) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: O=C(NCCCC[N@]1CC[N@@](c2ncccn2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001633010249.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633010249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001633010249 none O=C(NCCCC[N@]1CC[N@@](c2ncccn2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 2, 10, 15, 18, 29, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 3, 3, 3, 3, 3, 2, 10, 10, 18, 18, 18, 18, 27, 27, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 3, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `2' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249/2 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 2 (index: 990) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: O=C(NCCCC[N@]1CC[N@](c2ncccn2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001633010249.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001633010249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001633010249 none O=C(NCCCC[N@]1CC[N@](c2ncccn2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 2, 10, 16, 19, 31, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 3, 3, 3, 3, 3, 2, 10, 10, 19, 19, 19, 19, 28, 28, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 3, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `3' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249/3 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 3 (index: 991) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: O=C(NCCCC[N@]1CC[N@@](c2ncccn2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001633010249.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001633010249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001633010249 none O=C(NCCCC[N@]1CC[N@@](c2ncccn2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 8, 1, 1, 1, 8, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 2, 10, 16, 19, 31, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 3, 3, 3, 3, 3, 2, 10, 10, 19, 19, 19, 19, 28, 28, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 3, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001633010249 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 2: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249/2.* 3: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249/3.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633010249 Building ZINC001633195884 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633195884' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633195884 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633195884 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633195884/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633195884 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 992) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/992 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/992' -> `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)NCc1ccccc1CN1C(=O)NC2(CCCCC2)C1=O) `ZINC001633195884.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633195884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633195884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001633195884 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccccc1CN1C(=O)NC2(CCCCC2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 16, 16, 10, 16, 14, 16, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 16, 16, 10, 16, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 169 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633195884 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633195884/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633195884 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 993) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/993 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/993' -> `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)NCc1ccccc1CN1C(=O)NC2(CCCCC2)C1=O) `ZINC001633195884.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633195884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633195884/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001633195884 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccccc1CN1C(=O)NC2(CCCCC2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 15, 15, 10, 15, 13, 15, 27, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 15, 15, 10, 15, 27, 27, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 162 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633195884 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001633195884 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633195884/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633195884/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633195884 Building ZINC001633195884 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633195884' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633195884 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001633195884 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633195884/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633195884 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 992) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccccc1CN1C(=O)NC2(CCCCC2)C1=O) `ZINC001633195884.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001633195884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633195884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001633195884 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccccc1CN1C(=O)NC2(CCCCC2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 16, 16, 10, 16, 14, 16, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 16, 16, 10, 16, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 169 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633195884 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633195884/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633195884 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 993) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccccc1CN1C(=O)NC2(CCCCC2)C1=O) `ZINC001633195884.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001633195884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633195884/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001633195884 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccccc1CN1C(=O)NC2(CCCCC2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 15, 15, 10, 15, 13, 15, 27, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 15, 15, 10, 15, 27, 27, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 162 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633195884 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001633195884 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633195884/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633195884/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001633195884 Building ZINC001634121683 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634121683' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634121683 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634121683 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634121683/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634121683 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 994) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/994 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/994' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)N2CCN(Cc3ccccc3)CC2)CC1) `ZINC001634121683.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634121683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634121683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001634121683 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)N2CCN(Cc3ccccc3)CC2)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.3', 'N.am', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 6, 9, 20, 20, 20, 20, 28, 28, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 29, 29, 20, 20, 2, 2, 2, 2, 2, 2, 20, 20, 20, 20, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 29, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634121683 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634121683/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634121683 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 995) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/995 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/995' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)N2CCN(Cc3ccccc3)CC2)CC1) `ZINC001634121683.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634121683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634121683/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001634121683 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)N2CCN(Cc3ccccc3)CC2)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.3', 'N.am', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 5, 10, 23, 23, 23, 23, 28, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 28, 28, 23, 23, 2, 2, 2, 2, 2, 2, 23, 23, 23, 23, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28, 23, 23, 23, 23] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634121683 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001634121683 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634121683/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634121683/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634121683 Building ZINC001634121683 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634121683' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634121683 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634121683 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634121683/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634121683 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 994) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/994: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)N2CCN(Cc3ccccc3)CC2)CC1) `ZINC001634121683.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634121683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634121683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001634121683 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)N2CCN(Cc3ccccc3)CC2)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.3', 'N.am', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 6, 9, 20, 20, 20, 20, 28, 28, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 29, 29, 20, 20, 2, 2, 2, 2, 2, 2, 20, 20, 20, 20, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 29, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634121683 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634121683/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634121683 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 995) grep: /scratch/xiaobo/418326/xbt-8058088.46/working/3D/995: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)N2CCN(Cc3ccccc3)CC2)CC1) `ZINC001634121683.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634121683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634121683/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001634121683 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)N2CCN(Cc3ccccc3)CC2)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.3', 'N.am', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 5, 10, 23, 23, 23, 23, 28, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 28, 28, 23, 23, 2, 2, 2, 2, 2, 2, 23, 23, 23, 23, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28, 23, 23, 23, 23] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634121683 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001634121683 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634121683/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634121683/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634121683 Building ZINC001634230061 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634230061' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634230061 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634230061 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634230061/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634230061 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 996) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/996 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/996' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1CCN(C(=O)CC2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2)CC1) `ZINC001634230061.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634230061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634230061/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001634230061 none CN(C)C1CCN(C(=O)CC2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 39, 34, 34, 34, 26, 11, 26, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 34, 34, 39, 39, 39, 39, 39, 39, 34, 34, 34, 34, 34, 11, 11, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 34, 34, 34, 34] 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, 62, 63, 64, 65]) total number of confs: 122 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634230061 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634230061/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634230061 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 997) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/997 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/997' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1CCN(C(=O)CC2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2)CC1) `ZINC001634230061.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634230061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634230061/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001634230061 none CN(C)C1CCN(C(=O)CC2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 34, 34, 34, 28, 11, 28, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 34, 34, 38, 38, 38, 38, 38, 38, 34, 34, 34, 34, 34, 11, 11, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 34, 34, 34, 34] 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, 62, 63, 64, 65]) total number of confs: 126 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634230061 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001634230061 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634230061/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634230061/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634230061 Building ZINC001634230061 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634230061' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634230061 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634230061 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634230061/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634230061 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 996) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CN(C)C1CCN(C(=O)CC2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2)CC1) `ZINC001634230061.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634230061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634230061/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001634230061 none CN(C)C1CCN(C(=O)CC2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 39, 34, 34, 34, 26, 11, 26, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 34, 34, 39, 39, 39, 39, 39, 39, 34, 34, 34, 34, 34, 11, 11, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 34, 34, 34, 34] 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, 62, 63, 64, 65]) total number of confs: 122 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634230061 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634230061/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634230061 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 997) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CN(C)C1CCN(C(=O)CC2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2)CC1) `ZINC001634230061.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634230061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634230061/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001634230061 none CN(C)C1CCN(C(=O)CC2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 34, 34, 34, 28, 11, 28, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 34, 34, 38, 38, 38, 38, 38, 38, 34, 34, 34, 34, 34, 11, 11, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 34, 34, 34, 34] 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, 62, 63, 64, 65]) total number of confs: 126 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634230061 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001634230061 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634230061/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634230061/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634230061 Building ZINC001634391180 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634391180' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634391180 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634391180 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634391180/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634391180 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 998) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/998 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/998' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(CN3CCN(C(=O)OC(C)(C)C)CC3)cc2)cn1) `ZINC001634391180.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634391180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634391180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001634391180 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(CN3CCN(C(=O)OC(C)(C)C)CC3)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 10, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 2, 2, 2, 9, 16, 16, 13, 13, 35, 37, 37, 37, 37, 42, 42, 42, 42, 42, 42, 37, 37, 16, 16, 2, 2, 4, 4, 4, 4, 4, 2, 2, 9, 9, 16, 16, 35, 35, 37, 37, 37, 37, 42, 42, 42, 42, 42, 42, 42, 42, 42, 37, 37, 37, 37, 16, 16, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634391180 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634391180/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634391180 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 999) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/999 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/999' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(CN3CCN(C(=O)OC(C)(C)C)CC3)cc2)cn1) `ZINC001634391180.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634391180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634391180/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001634391180 none CCn1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(CN3CCN(C(=O)OC(C)(C)C)CC3)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 10, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 2, 2, 2, 9, 16, 16, 12, 12, 33, 36, 36, 36, 36, 41, 41, 41, 41, 41, 41, 36, 36, 16, 16, 3, 3, 5, 5, 5, 5, 5, 3, 2, 9, 9, 16, 16, 33, 33, 36, 36, 36, 36, 41, 41, 41, 41, 41, 41, 41, 41, 41, 36, 36, 36, 36, 16, 16, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634391180 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001634391180 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634391180/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634391180/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634391180 Building ZINC001634391180 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634391180' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634391180 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001634391180 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634391180/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634391180 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 998) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(CN3CCN(C(=O)OC(C)(C)C)CC3)cc2)cn1) `ZINC001634391180.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634391180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634391180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001634391180 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(CN3CCN(C(=O)OC(C)(C)C)CC3)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 10, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 2, 2, 2, 9, 16, 16, 13, 13, 35, 37, 37, 37, 37, 42, 42, 42, 42, 42, 42, 37, 37, 16, 16, 2, 2, 4, 4, 4, 4, 4, 2, 2, 9, 9, 16, 16, 35, 35, 37, 37, 37, 37, 42, 42, 42, 42, 42, 42, 42, 42, 42, 37, 37, 37, 37, 16, 16, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634391180 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 mkdir: created directory `1' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634391180/1 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634391180 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 1 (index: 999) grep: /scratch/xiaobo/418326/xbt-8058088.46/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: CCn1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(CN3CCN(C(=O)OC(C)(C)C)CC3)cc2)cn1) `ZINC001634391180.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001634391180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634391180/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001634391180 none CCn1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(CN3CCN(C(=O)OC(C)(C)C)CC3)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 10, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 2, 2, 2, 9, 16, 16, 12, 12, 33, 36, 36, 36, 36, 41, 41, 41, 41, 41, 41, 36, 36, 16, 16, 3, 3, 5, 5, 5, 5, 5, 3, 2, 9, 9, 16, 16, 33, 33, 36, 36, 36, 36, 41, 41, 41, 41, 41, 41, 41, 41, 41, 36, 36, 36, 36, 16, 16, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634391180 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001634391180 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634391180/0.* 1: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634391180/1.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634391180 Building ZINC001634723859 mkdir: created directory `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634723859' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634723859 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for ZINC001634723859 mkdir: created directory `0' /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634723859/0 /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634723859 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Protomer 0 (index: 1000) Found valid previously generated 3D confromation in /scratch/xiaobo/418326/xbt-8058088.46/working/3D/1000 `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/1000' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCN1CCCCC1)C1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CC1) `ZINC001634723859.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001634723859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634723859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001634723859 none O=C(NCCCN1CCCCC1)C1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 16, 20, 31, 38, 38, 38, 38, 38, 4, 4, 4, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 16, 16, 23, 23, 30, 31, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634723859 /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Finished preparing ZINC001634723859 Recording results /scratch/xiaobo/418326/xbt-8058088.46/working /scratch/xiaobo/418326/xbt-8058088.46 Appending to /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.* 0: /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634723859/0.* Removing working files in /scratch/xiaobo/418326/xbt-8058088.46/working/building/ZINC001634723859 /scratch/xiaobo/418326/xbt-8058088.46 Compressing combined databse files /scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.db2.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/xiaobo/418326/xbt-8058088.46/finished) ======================================================= Finalizing... removed `/scratch/xiaobo/418326/xbt-8058088.46/working/3D/1001' removed directory: `/scratch/xiaobo/418326/xbt-8058088.46/working/3D' rmdir: removing directory, `/scratch/xiaobo/418326/xbt-8058088.46/working/building' rmdir: removing directory, `/scratch/xiaobo/418326/xbt-8058088.46/working' /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/logs `/scratch/xiaobo/418326/xbt-8058088.46' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbt' `/scratch/xiaobo/418326/xbt-8058088.46/finished' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbt/finished' `/scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.db2.gz' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbt/finished/xbt.db2.gz' removed `/scratch/xiaobo/418326/xbt-8058088.46/finished/xbt.db2.gz' removed directory: `/scratch/xiaobo/418326/xbt-8058088.46/finished' removed directory: `/scratch/xiaobo/418326/xbt-8058088.46'